Starting phenix.real_space_refine on Thu Jul 31 11:28:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yni_39424/07_2025/8yni_39424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yni_39424/07_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_39424/07_2025/8yni_39424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yni_39424/07_2025/8yni_39424.map" model { file = "/net/cci-nas-00/data/ceres_data/8yni_39424/07_2025/8yni_39424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yni_39424/07_2025/8yni_39424.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.81, per 1000 atoms: 0.65 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: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.20 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: 3.47 Time building geometry restraints manager: 3.59 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: 3.700 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.030 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (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 HIS 0.002 0.000 HIS H 160 PHE 0.009 0.001 PHE A 120 TYR 0.006 0.001 TYR C 178 ARG 0.004 0.000 ARG I 61 Details of bonding type rmsd hydrogen bonds : bond 0.14655 ( 744) hydrogen bonds : angle 4.30651 ( 2217) covalent geometry : bond 0.00193 (13669) covalent geometry : angle 0.41891 (18315) *********************** 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 : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.8159 (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: 0.8662 (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: 0.8131 (t0) REVERT: B 178 TYR cc_start: 0.9089 (t80) cc_final: 0.8831 (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: 0.8691 (mmp) REVERT: H 99 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8193 (tm-30) 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: 0.8014 (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: 0.9125 (mtpp) REVERT: K 139 GLU cc_start: 0.8917 (tt0) cc_final: 0.8545 (tm-30) REVERT: L 54 ASP cc_start: 0.8284 (p0) cc_final: 0.7867 (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: 0.8917 (Cg_endo) REVERT: R 19 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8597 (mt-10) REVERT: R 35 LYS cc_start: 0.8804 (mttt) cc_final: 0.8288 (mtmm) REVERT: R 38 ARG cc_start: 0.8335 (ptp-110) cc_final: 0.8090 (ptp-170) REVERT: R 44 ASP cc_start: 0.9099 (m-30) cc_final: 0.8838 (p0) REVERT: R 51 GLU cc_start: 0.8049 (tp30) cc_final: 0.7755 (tp30) REVERT: R 64 ARG cc_start: 0.9276 (mtp180) cc_final: 0.9011 (mtm180) REVERT: Q 1 MET cc_start: 0.8420 (mtt) cc_final: 0.8058 (mmt) REVERT: Q 19 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8324 (mt-10) REVERT: Q 30 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7796 (mmt90) REVERT: Q 35 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8659 (mmtm) 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: 0.5770 (tmm) REVERT: G 119 TYR cc_start: 0.7979 (m-80) cc_final: 0.7680 (m-10) REVERT: G 158 ASN cc_start: 0.8975 (m-40) cc_final: 0.8771 (m-40) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.3555 time to fit residues: 193.0307 Evaluate side-chains 218 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 HIS J 88 HIS ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.085493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061746 restraints weight = 45977.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064032 restraints weight = 24266.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065568 restraints weight = 16268.644| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13669 Z= 0.200 Angle : 0.647 7.700 18315 Z= 0.328 Chirality : 0.040 0.204 2137 Planarity : 0.004 0.034 2331 Dihedral : 3.631 14.331 1809 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.62 % Allowed : 12.74 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1627 helix: 1.54 (0.15), residues: 1233 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS G 7 PHE 0.026 0.002 PHE Q 46 TYR 0.016 0.002 TYR H 119 ARG 0.006 0.000 ARG Q 77 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 744) hydrogen bonds : angle 4.16903 ( 2217) covalent geometry : bond 0.00467 (13669) covalent geometry : angle 0.64688 (18315) *********************** 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 260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9503 (mttt) cc_final: 0.9186 (mmtm) REVERT: A 86 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: A 107 GLN cc_start: 0.9256 (mt0) cc_final: 0.8982 (tt0) REVERT: B 137 MET cc_start: 0.6495 (mtm) cc_final: 0.6286 (mtm) REVERT: B 141 ASP cc_start: 0.8793 (t70) cc_final: 0.8304 (t0) REVERT: B 164 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7863 (t) REVERT: H 25 CYS cc_start: 0.8531 (m) cc_final: 0.8259 (t) REVERT: I 17 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8805 (mp0) REVERT: I 174 SER cc_start: 0.9236 (t) cc_final: 0.8973 (p) REVERT: J 99 GLU cc_start: 0.9196 (tp30) cc_final: 0.8844 (tm-30) REVERT: K 39 ASP cc_start: 0.8473 (m-30) cc_final: 0.8110 (m-30) REVERT: K 102 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8041 (tp30) REVERT: K 103 ASP cc_start: 0.8798 (m-30) cc_final: 0.8276 (t0) REVERT: K 106 LYS cc_start: 0.9268 (mttt) cc_final: 0.9053 (mtpp) REVERT: K 139 GLU cc_start: 0.9039 (tt0) cc_final: 0.8644 (tm-30) REVERT: L 51 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7526 (mm-30) REVERT: L 64 ARG cc_start: 0.9254 (mtt180) cc_final: 0.8934 (mtt180) REVERT: R 19 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8679 (mt-10) REVERT: R 38 ARG cc_start: 0.8504 (ptp-110) cc_final: 0.8170 (ptp-170) REVERT: R 64 ARG cc_start: 0.9221 (mtp180) cc_final: 0.8998 (mtm180) REVERT: Q 1 MET cc_start: 0.8559 (mtt) cc_final: 0.8210 (mmt) REVERT: Q 37 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6690 (mm-30) REVERT: Q 77 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8884 (ttp80) REVERT: G 1 MET cc_start: 0.6219 (ttp) cc_final: 0.5780 (ptt) REVERT: G 4 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8058 (mm-30) REVERT: G 40 LEU cc_start: 0.9437 (tt) cc_final: 0.9186 (tt) REVERT: G 119 TYR cc_start: 0.8110 (m-80) cc_final: 0.7693 (m-10) REVERT: G 158 ASN cc_start: 0.8950 (m-40) cc_final: 0.8728 (m-40) outliers start: 25 outliers final: 13 residues processed: 254 average time/residue: 0.3506 time to fit residues: 127.0189 Evaluate side-chains 210 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 30 ILE 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 L residue 39 VAL Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS L 52 GLN L 53 ASN G 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062367 restraints weight = 46756.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064764 restraints weight = 23810.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066346 restraints weight = 15692.487| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13669 Z= 0.141 Angle : 0.562 10.320 18315 Z= 0.287 Chirality : 0.037 0.155 2137 Planarity : 0.003 0.027 2331 Dihedral : 3.568 14.354 1809 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.81 % Allowed : 15.46 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1627 helix: 1.51 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 9 PHE 0.016 0.001 PHE I 114 TYR 0.017 0.001 TYR K 93 ARG 0.004 0.000 ARG Q 71 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 744) hydrogen bonds : angle 3.94008 ( 2217) covalent geometry : bond 0.00326 (13669) covalent geometry : angle 0.56206 (18315) *********************** 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 240 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9505 (mttt) cc_final: 0.9186 (mmtm) REVERT: A 64 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 107 GLN cc_start: 0.9240 (mt0) cc_final: 0.8965 (tt0) REVERT: A 110 GLU cc_start: 0.9062 (tp30) cc_final: 0.8856 (tp30) REVERT: B 141 ASP cc_start: 0.8728 (t70) cc_final: 0.8270 (t0) REVERT: B 146 MET cc_start: 0.8811 (mtm) cc_final: 0.8457 (mtm) REVERT: H 19 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8393 (mt-10) REVERT: H 25 CYS cc_start: 0.8511 (m) cc_final: 0.8279 (t) REVERT: H 111 SER cc_start: 0.9173 (m) cc_final: 0.8969 (t) REVERT: I 17 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8790 (mp0) REVERT: I 174 SER cc_start: 0.9231 (t) cc_final: 0.9012 (p) REVERT: J 88 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.6104 (m-70) REVERT: J 99 GLU cc_start: 0.9211 (tp30) cc_final: 0.8834 (tm-30) REVERT: K 39 ASP cc_start: 0.8477 (m-30) cc_final: 0.8099 (m-30) REVERT: K 102 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8041 (tp30) REVERT: K 103 ASP cc_start: 0.8791 (m-30) cc_final: 0.8237 (t0) REVERT: L 22 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8595 (mt-10) REVERT: L 51 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7466 (mm-30) REVERT: R 19 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8603 (mt-10) REVERT: R 38 ARG cc_start: 0.8526 (ptp-110) cc_final: 0.8169 (ptp-170) REVERT: R 64 ARG cc_start: 0.9294 (mtp180) cc_final: 0.9023 (mtm180) REVERT: Q 1 MET cc_start: 0.8518 (mtt) cc_final: 0.8176 (mmt) REVERT: Q 37 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6658 (mm-30) REVERT: Q 64 ARG cc_start: 0.9308 (ptp-170) cc_final: 0.8323 (ttm170) REVERT: Q 77 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8866 (ttp80) REVERT: G 4 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7968 (mp0) REVERT: G 74 MET cc_start: 0.8036 (mmm) cc_final: 0.7719 (ttt) REVERT: G 86 ASN cc_start: 0.7228 (t0) cc_final: 0.6965 (t0) REVERT: G 119 TYR cc_start: 0.8128 (m-80) cc_final: 0.7743 (m-10) REVERT: G 158 ASN cc_start: 0.8934 (m-40) cc_final: 0.8705 (m-40) outliers start: 28 outliers final: 16 residues processed: 233 average time/residue: 0.3530 time to fit residues: 117.0763 Evaluate side-chains 212 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 128 ILE 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 158 ASN Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain K residue 68 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 114 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 0.0040 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- 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 J 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.084883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.061274 restraints weight = 46227.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063466 restraints weight = 24659.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064949 restraints weight = 16665.860| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13669 Z= 0.183 Angle : 0.603 10.650 18315 Z= 0.308 Chirality : 0.038 0.168 2137 Planarity : 0.003 0.041 2331 Dihedral : 3.687 15.900 1809 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.46 % Allowed : 16.75 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1627 helix: 1.47 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 88 PHE 0.015 0.001 PHE B 143 TYR 0.021 0.002 TYR J 93 ARG 0.008 0.000 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 744) hydrogen bonds : angle 4.10650 ( 2217) covalent geometry : bond 0.00428 (13669) covalent geometry : angle 0.60344 (18315) *********************** 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 238 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9492 (mttt) cc_final: 0.9198 (mmtm) REVERT: A 107 GLN cc_start: 0.9239 (mt0) cc_final: 0.8970 (tt0) REVERT: A 110 GLU cc_start: 0.9036 (tp30) cc_final: 0.8796 (tp30) REVERT: B 141 ASP cc_start: 0.8797 (t70) cc_final: 0.8293 (t0) REVERT: H 19 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8428 (mt-10) REVERT: H 25 CYS cc_start: 0.8625 (m) cc_final: 0.8388 (t) REVERT: I 17 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8770 (mp0) REVERT: J 99 GLU cc_start: 0.9193 (tp30) cc_final: 0.8861 (tm-30) REVERT: J 140 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9282 (tttm) REVERT: K 39 ASP cc_start: 0.8444 (m-30) cc_final: 0.8099 (m-30) REVERT: K 97 MET cc_start: 0.8602 (mmt) cc_final: 0.8390 (mmm) REVERT: K 102 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8061 (tp30) REVERT: K 103 ASP cc_start: 0.8747 (m-30) cc_final: 0.8212 (t0) REVERT: L 2 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: L 51 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7504 (mm-30) REVERT: L 71 ARG cc_start: 0.9066 (mtm-85) cc_final: 0.8699 (ptp90) REVERT: R 19 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8717 (mt-10) REVERT: R 38 ARG cc_start: 0.8566 (ptp-110) cc_final: 0.8167 (ptp-170) REVERT: R 64 ARG cc_start: 0.9295 (mtp180) cc_final: 0.9040 (mtm180) REVERT: Q 1 MET cc_start: 0.8500 (mtt) cc_final: 0.8142 (mmt) REVERT: Q 37 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6872 (mm-30) REVERT: Q 64 ARG cc_start: 0.9145 (ptp-170) cc_final: 0.8505 (ttm170) REVERT: Q 77 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8829 (ttp80) REVERT: G 1 MET cc_start: 0.5746 (ttp) cc_final: 0.5222 (tmm) REVERT: G 4 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7933 (mp0) REVERT: G 86 ASN cc_start: 0.7259 (t0) cc_final: 0.7003 (t0) REVERT: G 119 TYR cc_start: 0.8149 (m-80) cc_final: 0.7823 (m-10) REVERT: G 158 ASN cc_start: 0.8941 (m-40) cc_final: 0.8697 (m-40) outliers start: 38 outliers final: 22 residues processed: 231 average time/residue: 0.2843 time to fit residues: 93.3768 Evaluate side-chains 220 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 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 158 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 140 LYS Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain L residue 2 ASP 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 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 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 160 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 54 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.086180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062758 restraints weight = 45955.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065031 restraints weight = 24225.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.066530 restraints weight = 16224.577| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13669 Z= 0.116 Angle : 0.548 9.699 18315 Z= 0.280 Chirality : 0.036 0.175 2137 Planarity : 0.003 0.030 2331 Dihedral : 3.606 18.355 1809 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.13 % Allowed : 18.37 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1627 helix: 1.57 (0.15), residues: 1226 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS Q 9 PHE 0.015 0.001 PHE B 143 TYR 0.019 0.001 TYR A 106 ARG 0.006 0.000 ARG L 30 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 744) hydrogen bonds : angle 3.77368 ( 2217) covalent geometry : bond 0.00265 (13669) covalent geometry : angle 0.54754 (18315) *********************** 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 246 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: A 39 LYS cc_start: 0.9499 (mttt) cc_final: 0.9215 (mmtm) REVERT: A 64 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 107 GLN cc_start: 0.9217 (mt0) cc_final: 0.8938 (tt0) REVERT: A 110 GLU cc_start: 0.8994 (tp30) cc_final: 0.8733 (tp30) REVERT: B 106 TYR cc_start: 0.8891 (t80) cc_final: 0.8542 (t80) REVERT: B 141 ASP cc_start: 0.8688 (t70) cc_final: 0.8196 (t0) REVERT: H 19 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8485 (mp0) REVERT: H 25 CYS cc_start: 0.8573 (m) cc_final: 0.8328 (t) REVERT: H 111 SER cc_start: 0.9223 (m) cc_final: 0.9008 (t) REVERT: I 17 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8755 (mp0) REVERT: I 97 MET cc_start: 0.9179 (mmp) cc_final: 0.8971 (mmm) REVERT: J 99 GLU cc_start: 0.9174 (tp30) cc_final: 0.8886 (tm-30) REVERT: K 39 ASP cc_start: 0.8448 (m-30) cc_final: 0.8163 (m-30) REVERT: K 102 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8011 (tp30) REVERT: K 103 ASP cc_start: 0.8631 (m-30) cc_final: 0.8172 (t0) REVERT: K 151 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8717 (tt) REVERT: L 2 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8535 (m-30) REVERT: L 22 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8663 (mt-10) REVERT: L 51 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7456 (mm-30) REVERT: L 69 SER cc_start: 0.8988 (m) cc_final: 0.8656 (p) REVERT: L 71 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8681 (ptp90) REVERT: R 19 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8571 (mt-10) REVERT: R 38 ARG cc_start: 0.8529 (ptp-110) cc_final: 0.8304 (ttp-170) REVERT: R 64 ARG cc_start: 0.9267 (mtp180) cc_final: 0.9032 (mtm180) REVERT: Q 1 MET cc_start: 0.8381 (mtt) cc_final: 0.8047 (mmt) REVERT: Q 37 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6991 (mm-30) REVERT: Q 64 ARG cc_start: 0.9098 (ptp-170) cc_final: 0.8497 (ttm170) REVERT: G 4 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7915 (mp0) REVERT: G 86 ASN cc_start: 0.7288 (t0) cc_final: 0.7025 (t0) REVERT: G 119 TYR cc_start: 0.8123 (m-80) cc_final: 0.7828 (m-10) REVERT: G 156 LEU cc_start: 0.9138 (mt) cc_final: 0.8922 (pp) REVERT: G 158 ASN cc_start: 0.8945 (m-40) cc_final: 0.8718 (m-40) outliers start: 33 outliers final: 21 residues processed: 239 average time/residue: 0.3092 time to fit residues: 107.2436 Evaluate side-chains 221 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE 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 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 39 VAL 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 91 SER Chi-restraints excluded: chain G residue 142 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 I 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064699 restraints weight = 47328.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066952 restraints weight = 26017.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068453 restraints weight = 17750.340| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3654 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= 0.106 Angle : 0.559 16.390 18315 Z= 0.281 Chirality : 0.036 0.174 2137 Planarity : 0.003 0.030 2331 Dihedral : 3.540 19.346 1809 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.13 % Allowed : 18.95 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1627 helix: 1.56 (0.16), residues: 1228 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS Q 9 PHE 0.022 0.001 PHE A 181 TYR 0.023 0.001 TYR C 101 ARG 0.008 0.000 ARG Q 77 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 744) hydrogen bonds : angle 3.62259 ( 2217) covalent geometry : bond 0.00236 (13669) covalent geometry : angle 0.55925 (18315) *********************** 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 245 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: A 39 LYS cc_start: 0.9447 (mttt) cc_final: 0.9232 (mmtm) REVERT: A 64 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 107 GLN cc_start: 0.9177 (mt0) cc_final: 0.8889 (tt0) REVERT: A 110 GLU cc_start: 0.8905 (tp30) cc_final: 0.8645 (tp30) REVERT: A 141 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: B 106 TYR cc_start: 0.8929 (t80) cc_final: 0.8344 (t80) REVERT: B 141 ASP cc_start: 0.8626 (t70) cc_final: 0.8162 (t0) REVERT: H 19 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8446 (mp0) REVERT: H 25 CYS cc_start: 0.8543 (m) cc_final: 0.8297 (t) REVERT: I 17 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8778 (mp0) REVERT: J 99 GLU cc_start: 0.9104 (tp30) cc_final: 0.8867 (tm-30) REVERT: K 39 ASP cc_start: 0.8392 (m-30) cc_final: 0.8088 (m-30) REVERT: K 102 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7851 (tp30) REVERT: K 103 ASP cc_start: 0.8563 (m-30) cc_final: 0.8155 (t0) REVERT: L 51 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7529 (mm-30) REVERT: L 69 SER cc_start: 0.8954 (m) cc_final: 0.8618 (p) REVERT: L 71 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8652 (ptp90) REVERT: R 19 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8496 (mt-10) REVERT: R 64 ARG cc_start: 0.9231 (mtp180) cc_final: 0.8774 (ptp-170) REVERT: R 77 ARG cc_start: 0.9276 (ttp80) cc_final: 0.8939 (tmm160) REVERT: Q 1 MET cc_start: 0.8354 (mtt) cc_final: 0.8018 (mmt) REVERT: Q 37 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7145 (mm-30) REVERT: Q 38 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7257 (tpt90) REVERT: Q 64 ARG cc_start: 0.9265 (ptp-170) cc_final: 0.8834 (ttm170) REVERT: Q 77 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8580 (ttp80) REVERT: G 4 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7904 (mp0) REVERT: G 86 ASN cc_start: 0.7384 (t0) cc_final: 0.7113 (t0) REVERT: G 116 MET cc_start: 0.8971 (mmm) cc_final: 0.8445 (mmt) REVERT: G 119 TYR cc_start: 0.8080 (m-80) cc_final: 0.7633 (m-80) REVERT: G 156 LEU cc_start: 0.9145 (mt) cc_final: 0.8928 (pp) REVERT: G 158 ASN cc_start: 0.8946 (m-40) cc_final: 0.8725 (m110) outliers start: 33 outliers final: 24 residues processed: 236 average time/residue: 0.2928 time to fit residues: 98.8980 Evaluate side-chains 227 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 LEU 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 158 ASN Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 13 LEU 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 11 GLU 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 L residue 17 SER Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 142 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.087731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064898 restraints weight = 47584.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067135 restraints weight = 26224.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068570 restraints weight = 17989.193| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3796 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= 0.107 Angle : 0.565 13.799 18315 Z= 0.283 Chirality : 0.036 0.175 2137 Planarity : 0.003 0.040 2331 Dihedral : 3.485 19.208 1809 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.20 % Allowed : 19.66 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1627 helix: 1.61 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.035 0.001 PHE Q 46 TYR 0.024 0.001 TYR C 101 ARG 0.006 0.000 ARG Q 77 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 744) hydrogen bonds : angle 3.60675 ( 2217) covalent geometry : bond 0.00242 (13669) covalent geometry : angle 0.56482 (18315) *********************** 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 243 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: A 39 LYS cc_start: 0.9478 (mttt) cc_final: 0.9235 (mmtm) REVERT: A 64 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 107 GLN cc_start: 0.9211 (mt0) cc_final: 0.8948 (tt0) REVERT: A 110 GLU cc_start: 0.8963 (tp30) cc_final: 0.8691 (tp30) REVERT: B 106 TYR cc_start: 0.8944 (t80) cc_final: 0.8378 (t80) REVERT: B 141 ASP cc_start: 0.8666 (t70) cc_final: 0.8171 (t0) REVERT: H 19 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8495 (mp0) REVERT: H 25 CYS cc_start: 0.8566 (m) cc_final: 0.8261 (t) REVERT: H 150 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8364 (t70) REVERT: I 17 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8771 (mp0) REVERT: J 99 GLU cc_start: 0.9156 (tp30) cc_final: 0.8842 (tm-30) REVERT: K 39 ASP cc_start: 0.8421 (m-30) cc_final: 0.8101 (m-30) REVERT: K 102 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7806 (tp30) REVERT: K 103 ASP cc_start: 0.8618 (m-30) cc_final: 0.8137 (t0) REVERT: K 151 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8670 (tt) REVERT: L 35 LYS cc_start: 0.9234 (mtmt) cc_final: 0.9020 (mttt) REVERT: L 48 MET cc_start: 0.9397 (tpp) cc_final: 0.9139 (tpp) REVERT: L 64 ARG cc_start: 0.9191 (mtm110) cc_final: 0.8661 (ptp-110) REVERT: L 69 SER cc_start: 0.8932 (m) cc_final: 0.8618 (p) REVERT: L 71 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8677 (ptp90) REVERT: R 19 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8447 (mt-10) REVERT: R 37 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8596 (tm-30) REVERT: R 64 ARG cc_start: 0.9348 (mtp180) cc_final: 0.8972 (mtm180) REVERT: R 77 ARG cc_start: 0.9306 (ttp80) cc_final: 0.8960 (tmm160) REVERT: Q 1 MET cc_start: 0.8415 (mtt) cc_final: 0.8081 (mmt) REVERT: Q 37 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6990 (mm-30) REVERT: Q 64 ARG cc_start: 0.9298 (ptp-170) cc_final: 0.8904 (ttm-80) REVERT: G 4 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7864 (mp0) REVERT: G 86 ASN cc_start: 0.7347 (t0) cc_final: 0.7144 (t0) REVERT: G 116 MET cc_start: 0.8940 (mmm) cc_final: 0.8447 (mmt) REVERT: G 119 TYR cc_start: 0.8056 (m-80) cc_final: 0.7613 (m-80) REVERT: G 156 LEU cc_start: 0.9127 (mt) cc_final: 0.8904 (pp) REVERT: G 158 ASN cc_start: 0.8954 (m-40) cc_final: 0.8729 (m110) outliers start: 34 outliers final: 25 residues processed: 234 average time/residue: 0.2785 time to fit residues: 91.9668 Evaluate side-chains 229 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 181 PHE 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 150 ASP 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 J residue 147 ASP 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 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 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 142 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 0.0050 chunk 138 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 114 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.088090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.065086 restraints weight = 47681.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.067397 restraints weight = 25659.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068921 restraints weight = 17380.989| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3906 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 : 0.574 13.453 18315 Z= 0.288 Chirality : 0.036 0.192 2137 Planarity : 0.003 0.034 2331 Dihedral : 3.508 30.368 1809 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.13 % Allowed : 19.86 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1627 helix: 1.58 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.025 0.001 PHE B 143 TYR 0.021 0.001 TYR C 101 ARG 0.012 0.000 ARG Q 77 Details of bonding type rmsd hydrogen bonds : bond 0.02701 ( 744) hydrogen bonds : angle 3.58930 ( 2217) covalent geometry : bond 0.00238 (13669) covalent geometry : angle 0.57403 (18315) *********************** 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 244 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: A 39 LYS cc_start: 0.9474 (mttt) cc_final: 0.9216 (mmtm) REVERT: A 64 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 107 GLN cc_start: 0.9208 (mt0) cc_final: 0.8937 (tt0) REVERT: A 110 GLU cc_start: 0.8959 (tp30) cc_final: 0.8690 (tp30) REVERT: B 106 TYR cc_start: 0.8969 (t80) cc_final: 0.8417 (t80) REVERT: B 141 ASP cc_start: 0.8650 (t70) cc_final: 0.8159 (t0) REVERT: B 146 MET cc_start: 0.8596 (mtm) cc_final: 0.8272 (mtm) REVERT: C 50 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8128 (tp30) REVERT: H 19 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8500 (mp0) REVERT: H 25 CYS cc_start: 0.8554 (m) cc_final: 0.8248 (t) REVERT: H 150 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8356 (t70) REVERT: I 17 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8767 (mp0) REVERT: I 97 MET cc_start: 0.9203 (mmp) cc_final: 0.8975 (mmm) REVERT: J 99 GLU cc_start: 0.9131 (tp30) cc_final: 0.8818 (tm-30) REVERT: K 39 ASP cc_start: 0.8430 (m-30) cc_final: 0.8103 (m-30) REVERT: K 102 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7821 (tp30) REVERT: K 103 ASP cc_start: 0.8622 (m-30) cc_final: 0.8136 (t0) REVERT: L 35 LYS cc_start: 0.9238 (mtmt) cc_final: 0.8877 (mttt) REVERT: L 48 MET cc_start: 0.9397 (tpp) cc_final: 0.9133 (tpp) REVERT: L 64 ARG cc_start: 0.9193 (mtm110) cc_final: 0.8650 (ptp-110) REVERT: L 69 SER cc_start: 0.8922 (m) cc_final: 0.8615 (p) REVERT: L 71 ARG cc_start: 0.9035 (mtm-85) cc_final: 0.8670 (ptp90) REVERT: R 19 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8513 (mt-10) REVERT: R 64 ARG cc_start: 0.9341 (mtp180) cc_final: 0.8921 (mpp-170) REVERT: R 77 ARG cc_start: 0.9300 (ttp80) cc_final: 0.9028 (tmm160) REVERT: Q 1 MET cc_start: 0.8389 (mtt) cc_final: 0.8051 (mmt) REVERT: Q 37 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7036 (mm-30) REVERT: Q 64 ARG cc_start: 0.9329 (ptp-170) cc_final: 0.9012 (ttm-80) REVERT: Q 70 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8727 (mm) REVERT: G 4 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7836 (mp0) REVERT: G 86 ASN cc_start: 0.7450 (t0) cc_final: 0.7157 (t0) REVERT: G 116 MET cc_start: 0.8954 (mmm) cc_final: 0.8496 (mmt) REVERT: G 119 TYR cc_start: 0.8043 (m-80) cc_final: 0.7629 (m-80) REVERT: G 156 LEU cc_start: 0.9135 (mt) cc_final: 0.8919 (pp) REVERT: G 158 ASN cc_start: 0.8956 (m-40) cc_final: 0.8732 (m110) outliers start: 33 outliers final: 23 residues processed: 233 average time/residue: 0.2750 time to fit residues: 90.7416 Evaluate side-chains 231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE 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 150 ASP Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU 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 30 ILE 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 Q residue 22 GLU Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 142 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 39 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 149 optimal weight: 0.0970 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.065032 restraints weight = 47211.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067295 restraints weight = 25543.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068790 restraints weight = 17429.520| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13669 Z= 0.111 Angle : 0.595 13.842 18315 Z= 0.297 Chirality : 0.036 0.179 2137 Planarity : 0.003 0.033 2331 Dihedral : 3.516 32.465 1809 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 1.88 % Allowed : 20.44 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1627 helix: 1.58 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS H 88 PHE 0.023 0.001 PHE A 181 TYR 0.021 0.001 TYR A 106 ARG 0.010 0.000 ARG Q 77 Details of bonding type rmsd hydrogen bonds : bond 0.02747 ( 744) hydrogen bonds : angle 3.62400 ( 2217) covalent geometry : bond 0.00254 (13669) covalent geometry : angle 0.59453 (18315) *********************** 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 236 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: A 39 LYS cc_start: 0.9477 (mttt) cc_final: 0.9199 (mmtm) REVERT: A 64 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 107 GLN cc_start: 0.9209 (mt0) cc_final: 0.8940 (tt0) REVERT: A 110 GLU cc_start: 0.8966 (tp30) cc_final: 0.8701 (tp30) REVERT: A 141 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8477 (m-30) REVERT: B 106 TYR cc_start: 0.8950 (t80) cc_final: 0.8398 (t80) REVERT: B 141 ASP cc_start: 0.8625 (t70) cc_final: 0.8142 (t0) REVERT: B 146 MET cc_start: 0.8553 (mtm) cc_final: 0.8081 (mtm) REVERT: C 50 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8095 (tp30) REVERT: H 19 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8493 (mp0) REVERT: H 25 CYS cc_start: 0.8562 (m) cc_final: 0.8252 (t) REVERT: H 150 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8354 (t70) REVERT: I 17 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8750 (mp0) REVERT: I 97 MET cc_start: 0.9210 (mmp) cc_final: 0.8983 (mmm) REVERT: J 99 GLU cc_start: 0.9125 (tp30) cc_final: 0.8818 (tm-30) REVERT: K 39 ASP cc_start: 0.8440 (m-30) cc_final: 0.8110 (m-30) REVERT: K 102 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7827 (tp30) REVERT: K 103 ASP cc_start: 0.8624 (m-30) cc_final: 0.8132 (t0) REVERT: K 151 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8669 (tt) REVERT: L 35 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8889 (mttt) REVERT: L 48 MET cc_start: 0.9389 (tpp) cc_final: 0.9132 (tpp) REVERT: L 64 ARG cc_start: 0.9190 (mtm110) cc_final: 0.8620 (ptp-110) REVERT: L 69 SER cc_start: 0.8921 (m) cc_final: 0.8616 (p) REVERT: L 71 ARG cc_start: 0.9029 (mtm-85) cc_final: 0.8670 (ptp90) REVERT: R 19 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8490 (mt-10) REVERT: R 64 ARG cc_start: 0.9357 (mtp180) cc_final: 0.8742 (mpp80) REVERT: R 77 ARG cc_start: 0.9299 (ttp80) cc_final: 0.9007 (tmm160) REVERT: Q 1 MET cc_start: 0.8394 (mtt) cc_final: 0.8072 (mmt) REVERT: Q 64 ARG cc_start: 0.9343 (ptp-170) cc_final: 0.9045 (ttm-80) REVERT: G 4 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7822 (mp0) REVERT: G 86 ASN cc_start: 0.7376 (t0) cc_final: 0.7091 (t0) REVERT: G 116 MET cc_start: 0.8927 (mmm) cc_final: 0.8454 (mmt) REVERT: G 119 TYR cc_start: 0.8038 (m-80) cc_final: 0.7621 (m-80) REVERT: G 156 LEU cc_start: 0.9140 (mt) cc_final: 0.8923 (pp) REVERT: G 158 ASN cc_start: 0.8963 (m-40) cc_final: 0.8735 (m-40) outliers start: 29 outliers final: 23 residues processed: 228 average time/residue: 0.2778 time to fit residues: 89.6127 Evaluate side-chains 225 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE 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 150 ASP 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 J residue 147 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 120 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 161 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.087918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065097 restraints weight = 47520.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067320 restraints weight = 26284.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.068795 restraints weight = 18080.933| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13669 Z= 0.115 Angle : 0.618 14.200 18315 Z= 0.309 Chirality : 0.037 0.214 2137 Planarity : 0.003 0.046 2331 Dihedral : 3.526 30.165 1809 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 1.88 % Allowed : 20.57 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1627 helix: 1.56 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS H 88 PHE 0.022 0.001 PHE A 181 TYR 0.019 0.001 TYR C 101 ARG 0.009 0.000 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 744) hydrogen bonds : angle 3.68865 ( 2217) covalent geometry : bond 0.00266 (13669) covalent geometry : angle 0.61821 (18315) ********************** 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 236 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: A 39 LYS cc_start: 0.9465 (mttt) cc_final: 0.9224 (mmtm) REVERT: A 64 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 107 GLN cc_start: 0.9199 (mt0) cc_final: 0.8917 (tt0) REVERT: A 110 GLU cc_start: 0.8949 (tp30) cc_final: 0.8681 (tp30) REVERT: B 1 MET cc_start: 0.6681 (tpt) cc_final: 0.6432 (tpp) REVERT: B 106 TYR cc_start: 0.8951 (t80) cc_final: 0.8462 (t80) REVERT: B 141 ASP cc_start: 0.8622 (t70) cc_final: 0.8159 (t0) REVERT: B 146 MET cc_start: 0.8478 (mtm) cc_final: 0.8085 (mtm) REVERT: C 50 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8058 (tp30) REVERT: H 19 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8488 (mp0) REVERT: H 25 CYS cc_start: 0.8575 (m) cc_final: 0.8253 (t) REVERT: H 74 MET cc_start: 0.8359 (ttm) cc_final: 0.7946 (ttt) REVERT: H 150 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8297 (t70) REVERT: I 17 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8746 (mp0) REVERT: I 97 MET cc_start: 0.9203 (mmp) cc_final: 0.8975 (mmm) REVERT: J 99 GLU cc_start: 0.9105 (tp30) cc_final: 0.8814 (tm-30) REVERT: K 39 ASP cc_start: 0.8430 (m-30) cc_final: 0.8105 (m-30) REVERT: K 102 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7815 (tp30) REVERT: K 103 ASP cc_start: 0.8566 (m-30) cc_final: 0.8111 (t0) REVERT: K 151 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8684 (tt) REVERT: L 35 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8889 (mttt) REVERT: L 48 MET cc_start: 0.9378 (tpp) cc_final: 0.9139 (tpp) REVERT: L 64 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8607 (ptp-110) REVERT: L 69 SER cc_start: 0.8897 (m) cc_final: 0.8612 (p) REVERT: L 71 ARG cc_start: 0.9043 (mtm-85) cc_final: 0.8687 (ptp90) REVERT: R 19 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8476 (mt-10) REVERT: R 64 ARG cc_start: 0.9363 (mtp180) cc_final: 0.8736 (mpp80) REVERT: R 77 ARG cc_start: 0.9275 (ttp80) cc_final: 0.8984 (tmm160) REVERT: Q 1 MET cc_start: 0.8408 (mtt) cc_final: 0.8083 (mmt) REVERT: Q 37 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6887 (mm-30) REVERT: Q 64 ARG cc_start: 0.9328 (ptp-170) cc_final: 0.9042 (ttm-80) REVERT: G 4 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7741 (mp0) REVERT: G 86 ASN cc_start: 0.7368 (t0) cc_final: 0.7076 (t0) REVERT: G 116 MET cc_start: 0.8920 (mmm) cc_final: 0.8508 (mmt) REVERT: G 156 LEU cc_start: 0.9148 (mt) cc_final: 0.8934 (pp) REVERT: G 158 ASN cc_start: 0.8969 (m-40) cc_final: 0.8743 (m-40) outliers start: 29 outliers final: 25 residues processed: 226 average time/residue: 0.2701 time to fit residues: 87.0500 Evaluate side-chains 231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU 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 124 LEU Chi-restraints excluded: chain B residue 128 ILE 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 150 ASP 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 J residue 147 ASP 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 Q residue 71 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 134 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.0060 chunk 108 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065081 restraints weight = 46186.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.067392 restraints weight = 24267.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068924 restraints weight = 16228.733| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13669 Z= 0.106 Angle : 0.611 13.858 18315 Z= 0.305 Chirality : 0.037 0.219 2137 Planarity : 0.003 0.031 2331 Dihedral : 3.495 30.140 1809 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 1.75 % Allowed : 20.96 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1627 helix: 1.53 (0.16), residues: 1237 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 59 PHE 0.043 0.001 PHE Q 46 TYR 0.019 0.001 TYR C 101 ARG 0.009 0.000 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.02535 ( 744) hydrogen bonds : angle 3.57139 ( 2217) covalent geometry : bond 0.00236 (13669) covalent geometry : angle 0.61117 (18315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4724.96 seconds wall clock time: 86 minutes 20.11 seconds (5180.11 seconds total)