Starting phenix.real_space_refine on Sun Nov 17 09:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yni_39424/11_2024/8yni_39424.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yni_39424/11_2024/8yni_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yni_39424/11_2024/8yni_39424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yni_39424/11_2024/8yni_39424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yni_39424/11_2024/8yni_39424.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yni_39424/11_2024/8yni_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-5513/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: 8.84, 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: 2.98 Conformation dependent library (CDL) restraints added in 1.8 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: 1.23 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: 3.75 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4552 1.34 - 1.46: 1951 1.46 - 1.58: 7037 1.58 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 13669 Sorted by residual: bond pdb=" N VAL Q 39 " pdb=" CA VAL Q 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.47e+00 bond pdb=" N ARG L 30 " pdb=" CA ARG L 30 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.33e-02 5.65e+03 6.31e+00 bond pdb=" N LYS C 51 " pdb=" CA LYS C 51 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 6.03e+00 bond pdb=" N GLU Q 37 " pdb=" CA GLU Q 37 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.33e-02 5.65e+03 5.04e+00 bond pdb=" N TYR C 29 " pdb=" CA TYR C 29 " ideal model delta sigma weight residual 1.456 1.481 -0.026 1.32e-02 5.74e+03 3.83e+00 ... (remaining 13664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 18129 1.63 - 3.26: 158 3.26 - 4.89: 24 4.89 - 6.52: 3 6.52 - 8.16: 1 Bond angle restraints: 18315 Sorted by residual: angle pdb=" N TYR C 29 " pdb=" CA TYR C 29 " pdb=" CB TYR C 29 " ideal model delta sigma weight residual 110.49 102.33 8.16 1.48e+00 4.57e-01 3.04e+01 angle pdb=" N LYS C 51 " pdb=" CA LYS C 51 " pdb=" C LYS C 51 " ideal model delta sigma weight residual 113.02 108.19 4.83 1.20e+00 6.94e-01 1.62e+01 angle pdb=" C LYS C 51 " pdb=" CA LYS C 51 " pdb=" CB LYS C 51 " ideal model delta sigma weight residual 110.37 116.48 -6.11 1.78e+00 3.16e-01 1.18e+01 angle pdb=" C GLU C 50 " pdb=" N LYS C 51 " pdb=" CA LYS C 51 " ideal model delta sigma weight residual 122.56 116.76 5.80 1.72e+00 3.38e-01 1.14e+01 angle pdb=" N ILE G 159 " pdb=" CA ILE G 159 " pdb=" C ILE G 159 " ideal model delta sigma weight residual 112.29 109.22 3.07 9.40e-01 1.13e+00 1.07e+01 ... (remaining 18310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7705 17.82 - 35.65: 824 35.65 - 53.47: 106 53.47 - 71.29: 12 71.29 - 89.11: 11 Dihedral angle restraints: 8658 sinusoidal: 3776 harmonic: 4882 Sorted by residual: dihedral pdb=" N TYR C 29 " pdb=" C TYR C 29 " pdb=" CA TYR C 29 " pdb=" CB TYR C 29 " ideal model delta harmonic sigma weight residual 122.80 113.65 9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CB GLU C 116 " pdb=" CG GLU C 116 " pdb=" CD GLU C 116 " pdb=" OE1 GLU C 116 " ideal model delta sinusoidal sigma weight residual 0.00 -84.79 84.79 1 3.00e+01 1.11e-03 9.70e+00 dihedral pdb=" CB MET K 97 " pdb=" CG MET K 97 " pdb=" SD MET K 97 " pdb=" CE MET K 97 " ideal model delta sinusoidal sigma weight residual 60.00 118.08 -58.08 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 8655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1608 0.038 - 0.076: 446 0.076 - 0.114: 73 0.114 - 0.152: 8 0.152 - 0.190: 2 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CA TYR C 29 " pdb=" N TYR C 29 " pdb=" C TYR C 29 " pdb=" CB TYR C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CB VAL C 150 " pdb=" CA VAL C 150 " pdb=" CG1 VAL C 150 " pdb=" CG2 VAL C 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA GLU Q 37 " pdb=" N GLU Q 37 " pdb=" C GLU Q 37 " pdb=" CB GLU Q 37 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 2134 not shown) Planarity restraints: 2331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 30 " -0.225 9.50e-02 1.11e+02 1.01e-01 6.24e+00 pdb=" NE ARG L 30 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG L 30 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 30 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG L 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO H 34 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 145 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO H 146 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " 0.017 5.00e-02 4.00e+02 ... (remaining 2328 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1211 2.74 - 3.28: 13630 3.28 - 3.82: 21321 3.82 - 4.36: 23510 4.36 - 4.90: 40505 Nonbonded interactions: 100177 Sorted by model distance: nonbonded pdb=" OH TYR B 29 " pdb=" O GLN B 97 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU L 22 " pdb=" NE2 HIS R 9 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU R 22 " pdb=" NE2 HIS Q 9 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR B 8 " pdb=" OE2 GLU B 12 " model vdw 2.276 3.040 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.287 3.040 ... (remaining 100172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 182) selection = (chain 'C' and resid 2 through 182) } ncs_group { reference = (chain 'G' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'H' and (resid 2 through 121 or resid 128 through 175)) selection = (chain 'I' and (resid 2 through 28 or resid 31 through 175)) selection = (chain 'J' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'K' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.530 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- 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= 0.128 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 *********************** 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 : 1.459 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: 0.3103 time to fit residues: 167.1889 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 : 1.819 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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= 0.301 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 *********************** 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 : 1.662 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 107 GLN cc_start: 0.9207 (mt0) cc_final: 0.8926 (tt0) REVERT: B 141 ASP cc_start: 0.8711 (t70) cc_final: 0.8235 (t0) REVERT: B 164 CYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7913 (t) REVERT: H 25 CYS cc_start: 0.8523 (m) cc_final: 0.8282 (t) REVERT: I 17 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8822 (mp0) REVERT: J 99 GLU cc_start: 0.9128 (tp30) cc_final: 0.8856 (tm-30) REVERT: K 39 ASP cc_start: 0.8371 (m-30) cc_final: 0.8044 (m-30) REVERT: K 102 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7910 (tp30) REVERT: K 103 ASP cc_start: 0.8637 (m-30) cc_final: 0.8247 (t0) REVERT: K 139 GLU cc_start: 0.8893 (tt0) cc_final: 0.8575 (tm-30) REVERT: L 22 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8753 (mt-10) REVERT: L 51 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7536 (mm-30) REVERT: L 64 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8866 (mtt180) REVERT: R 19 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8652 (mt-10) REVERT: R 38 ARG cc_start: 0.8402 (ptp-110) cc_final: 0.8086 (ptp-170) REVERT: Q 1 MET cc_start: 0.8492 (mtt) cc_final: 0.8123 (mmt) REVERT: Q 37 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6972 (mm-30) REVERT: Q 77 ARG cc_start: 0.9133 (ttp80) cc_final: 0.8884 (ttp80) REVERT: G 1 MET cc_start: 0.6260 (ttp) cc_final: 0.5837 (ptt) REVERT: G 4 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8057 (mm-30) REVERT: G 40 LEU cc_start: 0.9447 (tt) cc_final: 0.9175 (tt) REVERT: G 119 TYR cc_start: 0.8060 (m-80) cc_final: 0.7692 (m-10) REVERT: G 158 ASN cc_start: 0.8955 (m-40) cc_final: 0.8750 (m-40) outliers start: 25 outliers final: 13 residues processed: 254 average time/residue: 0.2794 time to fit residues: 100.5417 Evaluate side-chains 206 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain 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 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0470 chunk 122 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** L 53 ASN G 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13669 Z= 0.147 Angle : 0.535 10.497 18315 Z= 0.274 Chirality : 0.036 0.162 2137 Planarity : 0.003 0.026 2331 Dihedral : 3.468 13.497 1809 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.10 % Allowed : 15.39 % Favored : 83.51 % 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: 1.51 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 9 PHE 0.017 0.001 PHE I 114 TYR 0.019 0.001 TYR K 93 ARG 0.005 0.000 ARG Q 71 *********************** 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 244 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 141 ASP cc_start: 0.8599 (t70) cc_final: 0.8078 (t0) REVERT: B 146 MET cc_start: 0.8707 (mtm) cc_final: 0.8437 (mtm) REVERT: B 178 TYR cc_start: 0.9122 (t80) cc_final: 0.8794 (t80) REVERT: H 19 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8300 (mp0) REVERT: H 25 CYS cc_start: 0.8417 (m) cc_final: 0.8201 (t) REVERT: H 111 SER cc_start: 0.9292 (m) cc_final: 0.9071 (t) REVERT: I 17 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8775 (mp0) REVERT: I 36 ASN cc_start: 0.8536 (t0) cc_final: 0.8225 (t0) REVERT: J 99 GLU cc_start: 0.9103 (tp30) cc_final: 0.8850 (tm-30) REVERT: J 116 MET cc_start: 0.8793 (mmt) cc_final: 0.8102 (mmt) REVERT: K 39 ASP cc_start: 0.8379 (m-30) cc_final: 0.8054 (m-30) REVERT: K 67 LEU cc_start: 0.9478 (mt) cc_final: 0.9277 (mp) REVERT: K 102 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7892 (tp30) REVERT: K 103 ASP cc_start: 0.8549 (m-30) cc_final: 0.8156 (t0) REVERT: L 22 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8705 (mt-10) REVERT: L 51 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7456 (mm-30) REVERT: R 19 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8590 (mt-10) REVERT: R 38 ARG cc_start: 0.8382 (ptp-110) cc_final: 0.8070 (ptp-170) REVERT: R 64 ARG cc_start: 0.9290 (mtm180) cc_final: 0.8645 (mpp80) REVERT: Q 1 MET cc_start: 0.8361 (mtt) cc_final: 0.8013 (mmt) REVERT: Q 37 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6964 (mm-30) REVERT: Q 64 ARG cc_start: 0.9292 (ptp-170) cc_final: 0.8780 (mtt90) REVERT: Q 77 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8858 (ttp80) REVERT: G 1 MET cc_start: 0.6228 (ttp) cc_final: 0.6021 (ttp) REVERT: G 4 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7965 (mp0) REVERT: G 74 MET cc_start: 0.7981 (mmm) cc_final: 0.7687 (ttt) REVERT: G 86 ASN cc_start: 0.7310 (t0) cc_final: 0.7017 (t0) REVERT: G 119 TYR cc_start: 0.8089 (m-80) cc_final: 0.7769 (m-10) REVERT: G 158 ASN cc_start: 0.8937 (m-40) cc_final: 0.8732 (m-40) outliers start: 17 outliers final: 11 residues processed: 240 average time/residue: 0.2719 time to fit residues: 92.5694 Evaluate side-chains 209 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR 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 120 MET Chi-restraints excluded: chain Q residue 22 GLU 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 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3327 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= 0.160 Angle : 0.540 10.489 18315 Z= 0.278 Chirality : 0.036 0.208 2137 Planarity : 0.003 0.039 2331 Dihedral : 3.452 15.952 1809 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.68 % Allowed : 16.04 % Favored : 82.28 % 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: 1.36 (0.21), residues: 1627 helix: 1.56 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 9 PHE 0.012 0.001 PHE A 181 TYR 0.020 0.001 TYR C 101 ARG 0.008 0.000 ARG Q 78 *********************** 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 239 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 110 GLU cc_start: 0.8585 (tp30) cc_final: 0.8135 (tp30) REVERT: B 106 TYR cc_start: 0.8797 (t80) cc_final: 0.8496 (t80) REVERT: B 141 ASP cc_start: 0.8587 (t70) cc_final: 0.8083 (t0) REVERT: B 178 TYR cc_start: 0.9156 (t80) cc_final: 0.8829 (t80) REVERT: H 19 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8364 (mp0) REVERT: H 25 CYS cc_start: 0.8481 (m) cc_final: 0.8230 (t) REVERT: I 17 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8778 (mp0) REVERT: J 99 GLU cc_start: 0.9117 (tp30) cc_final: 0.8876 (tm-30) REVERT: J 140 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9274 (tttm) REVERT: K 39 ASP cc_start: 0.8410 (m-30) cc_final: 0.8082 (m-30) REVERT: K 102 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7829 (tp30) REVERT: K 103 ASP cc_start: 0.8557 (m-30) cc_final: 0.8193 (t0) REVERT: L 2 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: L 22 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8689 (mt-10) REVERT: L 51 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7436 (mm-30) REVERT: L 64 ARG cc_start: 0.9128 (mtm110) cc_final: 0.8890 (mtt-85) REVERT: L 69 SER cc_start: 0.8966 (m) cc_final: 0.8657 (p) REVERT: R 19 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8660 (mt-10) REVERT: R 37 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8365 (tm-30) REVERT: R 64 ARG cc_start: 0.9339 (mtm180) cc_final: 0.8627 (mpp80) REVERT: Q 1 MET cc_start: 0.8379 (mtt) cc_final: 0.8024 (mmt) REVERT: Q 37 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7006 (mm-30) REVERT: Q 48 MET cc_start: 0.9297 (ttm) cc_final: 0.9082 (ttm) REVERT: Q 64 ARG cc_start: 0.9294 (ptp-170) cc_final: 0.8509 (ttm170) REVERT: Q 77 ARG cc_start: 0.9164 (ttp80) cc_final: 0.8681 (ttp80) REVERT: G 4 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7926 (mp0) REVERT: G 86 ASN cc_start: 0.7238 (t0) cc_final: 0.6940 (t0) REVERT: G 119 TYR cc_start: 0.8092 (m-80) cc_final: 0.7798 (m-10) REVERT: G 158 ASN cc_start: 0.8938 (m-40) cc_final: 0.8725 (m-40) outliers start: 26 outliers final: 18 residues processed: 233 average time/residue: 0.2848 time to fit residues: 94.4678 Evaluate side-chains 224 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 C residue 10 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 140 LYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 chunk 116 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN I 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13669 Z= 0.162 Angle : 0.534 9.416 18315 Z= 0.274 Chirality : 0.036 0.182 2137 Planarity : 0.003 0.031 2331 Dihedral : 3.482 20.447 1809 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.13 % Allowed : 16.82 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1627 helix: 1.54 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -1.16 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS J 7 PHE 0.017 0.001 PHE A 181 TYR 0.023 0.001 TYR J 93 ARG 0.007 0.000 ARG Q 78 *********************** 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 249 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8251 (tm-30) REVERT: A 110 GLU cc_start: 0.8630 (tp30) cc_final: 0.8124 (tp30) REVERT: B 106 TYR cc_start: 0.8790 (t80) cc_final: 0.8070 (t80) REVERT: B 141 ASP cc_start: 0.8581 (t70) cc_final: 0.8100 (t0) REVERT: B 178 TYR cc_start: 0.9169 (t80) cc_final: 0.8844 (t80) REVERT: H 19 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8430 (mp0) REVERT: H 25 CYS cc_start: 0.8513 (m) cc_final: 0.8264 (t) REVERT: I 17 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8780 (mp0) REVERT: I 97 MET cc_start: 0.9127 (mmp) cc_final: 0.8917 (mmm) REVERT: J 99 GLU cc_start: 0.9121 (tp30) cc_final: 0.8879 (tm-30) REVERT: K 39 ASP cc_start: 0.8397 (m-30) cc_final: 0.8069 (m-30) REVERT: K 102 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7748 (tp30) REVERT: K 103 ASP cc_start: 0.8552 (m-30) cc_final: 0.8183 (t0) REVERT: L 22 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8687 (mt-10) REVERT: L 51 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7549 (mm-30) REVERT: L 64 ARG cc_start: 0.9131 (mtm110) cc_final: 0.8690 (ptp-110) REVERT: L 69 SER cc_start: 0.8953 (m) cc_final: 0.8612 (p) REVERT: L 71 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.8658 (ptp90) REVERT: R 19 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8517 (mt-10) REVERT: R 64 ARG cc_start: 0.9369 (mtm180) cc_final: 0.8741 (mpp80) REVERT: Q 1 MET cc_start: 0.8359 (mtt) cc_final: 0.8005 (mmt) REVERT: Q 48 MET cc_start: 0.9304 (ttm) cc_final: 0.9104 (ttm) REVERT: Q 64 ARG cc_start: 0.9148 (ptp-170) cc_final: 0.8762 (ttm170) REVERT: G 4 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7917 (mp0) REVERT: G 86 ASN cc_start: 0.7202 (t0) cc_final: 0.6913 (t0) REVERT: G 119 TYR cc_start: 0.8066 (m-80) cc_final: 0.7809 (m-10) REVERT: G 156 LEU cc_start: 0.9195 (mt) cc_final: 0.8977 (pp) REVERT: G 158 ASN cc_start: 0.8942 (m-40) cc_final: 0.8736 (m-40) outliers start: 33 outliers final: 21 residues processed: 240 average time/residue: 0.2926 time to fit residues: 99.4716 Evaluate side-chains 226 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 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 I residue 74 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain R residue 59 HIS Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 0.0770 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13669 Z= 0.169 Angle : 0.569 15.821 18315 Z= 0.283 Chirality : 0.036 0.172 2137 Planarity : 0.003 0.029 2331 Dihedral : 3.493 23.961 1809 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.94 % Allowed : 17.98 % Favored : 80.08 % 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: 1.32 (0.21), residues: 1627 helix: 1.53 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -1.23 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 9 PHE 0.014 0.001 PHE A 181 TYR 0.024 0.001 TYR J 93 ARG 0.008 0.000 ARG Q 77 *********************** 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 246 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 110 GLU cc_start: 0.8629 (tp30) cc_final: 0.8141 (tp30) REVERT: B 106 TYR cc_start: 0.8828 (t80) cc_final: 0.8136 (t80) REVERT: B 141 ASP cc_start: 0.8592 (t70) cc_final: 0.8145 (t0) REVERT: B 178 TYR cc_start: 0.9179 (t80) cc_final: 0.8857 (t80) REVERT: H 19 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8407 (mp0) REVERT: H 25 CYS cc_start: 0.8535 (m) cc_final: 0.8245 (t) REVERT: H 116 MET cc_start: 0.8525 (mmt) cc_final: 0.8319 (mmp) REVERT: I 17 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8781 (mp0) REVERT: J 99 GLU cc_start: 0.9125 (tp30) cc_final: 0.8882 (tm-30) REVERT: K 10 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8535 (tm-30) REVERT: K 39 ASP cc_start: 0.8380 (m-30) cc_final: 0.8058 (m-30) REVERT: K 102 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7822 (tp30) REVERT: K 103 ASP cc_start: 0.8566 (m-30) cc_final: 0.8186 (t0) REVERT: K 151 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8727 (tt) REVERT: L 22 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8622 (mt-10) REVERT: L 51 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7543 (mm-30) REVERT: L 64 ARG cc_start: 0.9138 (mtm110) cc_final: 0.8708 (ptp-110) REVERT: L 69 SER cc_start: 0.8940 (m) cc_final: 0.8592 (p) REVERT: L 71 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8643 (ptp90) REVERT: R 19 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8501 (mt-10) REVERT: R 64 ARG cc_start: 0.9371 (mtm180) cc_final: 0.8661 (mpp80) REVERT: Q 1 MET cc_start: 0.8317 (mtt) cc_final: 0.8000 (mmt) REVERT: Q 64 ARG cc_start: 0.9208 (ptp-170) cc_final: 0.8920 (ttm170) REVERT: Q 77 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8616 (ttp80) REVERT: G 4 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7890 (mp0) REVERT: G 86 ASN cc_start: 0.7360 (t0) cc_final: 0.7095 (t0) REVERT: G 116 MET cc_start: 0.9043 (mmm) cc_final: 0.8477 (mmt) REVERT: G 119 TYR cc_start: 0.8047 (m-80) cc_final: 0.7606 (m-80) REVERT: G 156 LEU cc_start: 0.9182 (mt) cc_final: 0.8960 (pp) REVERT: G 158 ASN cc_start: 0.8936 (m-40) cc_final: 0.8734 (m110) outliers start: 30 outliers final: 22 residues processed: 234 average time/residue: 0.3167 time to fit residues: 105.7445 Evaluate side-chains 226 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 124 LEU 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 I residue 74 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain R residue 59 HIS Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13669 Z= 0.242 Angle : 0.619 13.384 18315 Z= 0.311 Chirality : 0.038 0.177 2137 Planarity : 0.003 0.039 2331 Dihedral : 3.663 23.307 1809 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.39 % Allowed : 19.02 % Favored : 78.59 % 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: 1.25 (0.21), residues: 1627 helix: 1.55 (0.16), residues: 1225 sheet: None (None), residues: 0 loop : -1.40 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS Q 9 PHE 0.033 0.002 PHE Q 46 TYR 0.022 0.001 TYR J 93 ARG 0.011 0.000 ARG Q 78 *********************** 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 240 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 110 GLU cc_start: 0.8713 (tp30) cc_final: 0.8233 (tp30) REVERT: B 106 TYR cc_start: 0.8872 (t80) cc_final: 0.8593 (t80) REVERT: B 141 ASP cc_start: 0.8655 (t70) cc_final: 0.8214 (t0) REVERT: B 178 TYR cc_start: 0.9212 (t80) cc_final: 0.8896 (t80) REVERT: H 19 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8440 (mt-10) REVERT: H 25 CYS cc_start: 0.8661 (m) cc_final: 0.8395 (t) REVERT: I 17 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8744 (mp0) REVERT: I 97 MET cc_start: 0.9177 (mmp) cc_final: 0.8955 (mmm) REVERT: J 99 GLU cc_start: 0.9145 (tp30) cc_final: 0.8866 (tm-30) REVERT: K 10 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8621 (tm-30) REVERT: K 39 ASP cc_start: 0.8381 (m-30) cc_final: 0.8067 (m-30) REVERT: K 102 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7911 (tp30) REVERT: K 103 ASP cc_start: 0.8580 (m-30) cc_final: 0.8174 (t0) REVERT: K 151 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8902 (tt) REVERT: L 22 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8623 (mt-10) REVERT: L 51 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7502 (mm-30) REVERT: L 69 SER cc_start: 0.8978 (m) cc_final: 0.8639 (p) REVERT: L 71 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8659 (ptp90) REVERT: R 19 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8483 (mt-10) REVERT: R 64 ARG cc_start: 0.9337 (mtm180) cc_final: 0.8781 (ptp-170) REVERT: Q 1 MET cc_start: 0.8436 (mtt) cc_final: 0.8091 (mmt) REVERT: Q 64 ARG cc_start: 0.9260 (ptp-170) cc_final: 0.8882 (ttm170) REVERT: Q 77 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8611 (tmm-80) REVERT: G 4 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7833 (mp0) REVERT: G 44 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8987 (mm) REVERT: G 86 ASN cc_start: 0.7360 (t0) cc_final: 0.7083 (t0) REVERT: G 116 MET cc_start: 0.9052 (mmm) cc_final: 0.8507 (mmt) REVERT: G 119 TYR cc_start: 0.8002 (m-80) cc_final: 0.7611 (m-80) REVERT: G 156 LEU cc_start: 0.9195 (mt) cc_final: 0.8976 (pp) REVERT: G 158 ASN cc_start: 0.8937 (m-40) cc_final: 0.8711 (m-40) outliers start: 37 outliers final: 26 residues processed: 228 average time/residue: 0.2744 time to fit residues: 89.3722 Evaluate side-chains 221 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 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 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 74 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 17 SER 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 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3910 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= 0.172 Angle : 0.597 13.531 18315 Z= 0.300 Chirality : 0.037 0.202 2137 Planarity : 0.003 0.029 2331 Dihedral : 3.607 26.424 1809 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.81 % Allowed : 19.86 % Favored : 78.33 % 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: 1.22 (0.21), residues: 1627 helix: 1.55 (0.16), residues: 1221 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 9 PHE 0.011 0.001 PHE B 143 TYR 0.026 0.001 TYR C 101 ARG 0.006 0.000 ARG Q 77 *********************** 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 230 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 110 GLU cc_start: 0.8679 (tp30) cc_final: 0.8142 (tp30) REVERT: B 1 MET cc_start: 0.6856 (tpt) cc_final: 0.6583 (tpp) REVERT: B 106 TYR cc_start: 0.8882 (t80) cc_final: 0.8270 (t80) REVERT: B 141 ASP cc_start: 0.8623 (t70) cc_final: 0.8194 (t0) REVERT: B 178 TYR cc_start: 0.9191 (t80) cc_final: 0.8888 (t80) REVERT: H 19 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8475 (mp0) REVERT: H 25 CYS cc_start: 0.8590 (m) cc_final: 0.8316 (t) REVERT: I 17 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8754 (mp0) REVERT: I 97 MET cc_start: 0.9165 (mmp) cc_final: 0.8949 (mmm) REVERT: J 99 GLU cc_start: 0.9120 (tp30) cc_final: 0.8872 (tm-30) REVERT: K 10 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8550 (tm-30) REVERT: K 39 ASP cc_start: 0.8365 (m-30) cc_final: 0.8051 (m-30) REVERT: K 102 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7914 (tp30) REVERT: K 103 ASP cc_start: 0.8517 (m-30) cc_final: 0.8142 (t0) REVERT: K 151 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8759 (tt) REVERT: L 22 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8630 (mt-10) REVERT: L 51 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7474 (mm-30) REVERT: L 64 ARG cc_start: 0.9146 (mtm110) cc_final: 0.8674 (ptp-110) REVERT: L 69 SER cc_start: 0.8911 (m) cc_final: 0.8599 (p) REVERT: L 71 ARG cc_start: 0.9012 (mtm-85) cc_final: 0.8632 (ptp90) REVERT: R 19 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8530 (mt-10) REVERT: R 22 GLU cc_start: 0.9162 (tt0) cc_final: 0.8899 (tp30) REVERT: R 64 ARG cc_start: 0.9330 (mtm180) cc_final: 0.8742 (ptp-170) REVERT: Q 1 MET cc_start: 0.8370 (mtt) cc_final: 0.8014 (mmt) REVERT: Q 37 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6983 (mm-30) REVERT: Q 64 ARG cc_start: 0.9246 (ptp-170) cc_final: 0.8875 (ttm170) REVERT: Q 77 ARG cc_start: 0.8973 (ttp80) cc_final: 0.8695 (tmm-80) REVERT: G 4 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7799 (mp0) REVERT: G 44 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9030 (mm) REVERT: G 86 ASN cc_start: 0.7307 (t0) cc_final: 0.7025 (t0) REVERT: G 116 MET cc_start: 0.9120 (mmm) cc_final: 0.8643 (mmt) REVERT: G 119 TYR cc_start: 0.7976 (m-80) cc_final: 0.7598 (m-80) REVERT: G 156 LEU cc_start: 0.9195 (mt) cc_final: 0.8980 (pp) REVERT: G 158 ASN cc_start: 0.8946 (m-40) cc_final: 0.8741 (m-40) outliers start: 28 outliers final: 22 residues processed: 222 average time/residue: 0.2937 time to fit residues: 91.8368 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 : 1.896 ------------------------------------------------------------------------------- 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 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 I residue 74 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 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 G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.3980 chunk 136 optimal weight: 7.9990 chunk 145 optimal weight: 0.0000 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4037 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= 0.153 Angle : 0.598 13.943 18315 Z= 0.300 Chirality : 0.037 0.179 2137 Planarity : 0.003 0.028 2331 Dihedral : 3.592 29.887 1809 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 1.49 % Allowed : 19.86 % Favored : 78.65 % 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: 1.19 (0.21), residues: 1627 helix: 1.50 (0.16), residues: 1228 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS L 9 PHE 0.012 0.001 PHE A 181 TYR 0.023 0.001 TYR C 101 ARG 0.007 0.000 ARG R 77 *********************** 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 237 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 110 GLU cc_start: 0.8613 (tp30) cc_final: 0.8064 (tp30) REVERT: B 106 TYR cc_start: 0.8915 (t80) cc_final: 0.8442 (t80) REVERT: B 128 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7321 (tp) REVERT: B 141 ASP cc_start: 0.8589 (t70) cc_final: 0.8142 (t0) REVERT: B 146 MET cc_start: 0.8433 (mtm) cc_final: 0.8181 (mtm) REVERT: B 178 TYR cc_start: 0.9160 (t80) cc_final: 0.8869 (t80) REVERT: H 19 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8454 (mp0) REVERT: H 25 CYS cc_start: 0.8545 (m) cc_final: 0.8235 (t) REVERT: I 17 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8762 (mp0) REVERT: K 10 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8531 (tm-30) REVERT: K 39 ASP cc_start: 0.8361 (m-30) cc_final: 0.8033 (m-30) REVERT: K 102 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7865 (tp30) REVERT: K 103 ASP cc_start: 0.8512 (m-30) cc_final: 0.8105 (t0) REVERT: L 22 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8645 (mt-10) REVERT: L 64 ARG cc_start: 0.9154 (mtm110) cc_final: 0.8648 (ptp-110) REVERT: L 69 SER cc_start: 0.8874 (m) cc_final: 0.8589 (p) REVERT: L 71 ARG cc_start: 0.8995 (mtm-85) cc_final: 0.8621 (ptp90) REVERT: R 19 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8469 (mt-10) REVERT: R 77 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8926 (tmm160) REVERT: Q 1 MET cc_start: 0.8353 (mtt) cc_final: 0.7998 (mmt) REVERT: Q 37 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6999 (mm-30) REVERT: Q 64 ARG cc_start: 0.9228 (ptp-170) cc_final: 0.8796 (ttm170) REVERT: Q 77 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8646 (tmm-80) REVERT: G 4 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7761 (mp0) REVERT: G 44 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9035 (mm) REVERT: G 86 ASN cc_start: 0.7301 (t0) cc_final: 0.7006 (t0) REVERT: G 116 MET cc_start: 0.9077 (mmm) cc_final: 0.8633 (mmt) REVERT: G 156 LEU cc_start: 0.9192 (mt) cc_final: 0.8981 (pp) REVERT: G 158 ASN cc_start: 0.8944 (m-40) cc_final: 0.8736 (m110) outliers start: 23 outliers final: 19 residues processed: 229 average time/residue: 0.3097 time to fit residues: 100.6543 Evaluate side-chains 225 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 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 110 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET 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 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN H 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13669 Z= 0.167 Angle : 0.623 13.975 18315 Z= 0.313 Chirality : 0.037 0.178 2137 Planarity : 0.003 0.029 2331 Dihedral : 3.587 29.849 1809 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 19.92 % Favored : 78.53 % 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: 1.19 (0.22), residues: 1627 helix: 1.46 (0.16), residues: 1236 sheet: None (None), residues: 0 loop : -1.36 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS H 88 PHE 0.012 0.001 PHE A 181 TYR 0.022 0.001 TYR C 101 ARG 0.007 0.000 ARG R 77 ********************** 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 227 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 110 GLU cc_start: 0.8625 (tp30) cc_final: 0.8066 (tp30) REVERT: A 143 PHE cc_start: 0.9235 (m-10) cc_final: 0.9016 (m-80) REVERT: B 1 MET cc_start: 0.6821 (tpt) cc_final: 0.6560 (tpp) REVERT: B 106 TYR cc_start: 0.8857 (t80) cc_final: 0.8377 (t80) REVERT: B 141 ASP cc_start: 0.8542 (t70) cc_final: 0.8119 (t0) REVERT: B 146 MET cc_start: 0.8346 (mtm) cc_final: 0.8105 (mtm) REVERT: B 178 TYR cc_start: 0.9163 (t80) cc_final: 0.8872 (t80) REVERT: H 19 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8446 (mp0) REVERT: H 25 CYS cc_start: 0.8530 (m) cc_final: 0.8182 (t) REVERT: H 74 MET cc_start: 0.8187 (ttm) cc_final: 0.7844 (ttt) REVERT: I 17 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8760 (mp0) REVERT: K 10 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8536 (tm-30) REVERT: K 39 ASP cc_start: 0.8365 (m-30) cc_final: 0.8036 (m-30) REVERT: K 102 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7972 (tp30) REVERT: K 103 ASP cc_start: 0.8541 (m-30) cc_final: 0.8113 (t0) REVERT: K 151 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8724 (tt) REVERT: L 22 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8680 (mt-10) REVERT: L 64 ARG cc_start: 0.9123 (mtm110) cc_final: 0.8593 (ptp-110) REVERT: L 69 SER cc_start: 0.8865 (m) cc_final: 0.8583 (p) REVERT: L 71 ARG cc_start: 0.8995 (mtm-85) cc_final: 0.8622 (ptp90) REVERT: R 19 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8434 (mt-10) REVERT: R 64 ARG cc_start: 0.9329 (mtm180) cc_final: 0.8579 (mtm110) REVERT: R 77 ARG cc_start: 0.9239 (ttp80) cc_final: 0.8910 (tmm160) REVERT: Q 1 MET cc_start: 0.8380 (mtt) cc_final: 0.8024 (mmt) REVERT: Q 37 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6990 (mm-30) REVERT: Q 64 ARG cc_start: 0.9326 (ptp-170) cc_final: 0.8948 (ttm-80) REVERT: G 4 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7741 (mp0) REVERT: G 44 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9039 (mm) REVERT: G 86 ASN cc_start: 0.7270 (t0) cc_final: 0.6981 (t0) REVERT: G 116 MET cc_start: 0.9042 (mmm) cc_final: 0.8622 (mmt) REVERT: G 156 LEU cc_start: 0.9194 (mt) cc_final: 0.8984 (pp) REVERT: G 158 ASN cc_start: 0.8949 (m-40) cc_final: 0.8740 (m110) outliers start: 24 outliers final: 21 residues processed: 219 average time/residue: 0.2856 time to fit residues: 88.2771 Evaluate side-chains 220 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 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 110 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain 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 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN H 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063495 restraints weight = 45510.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065825 restraints weight = 23957.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067364 restraints weight = 16093.743| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13669 Z= 0.181 Angle : 0.630 14.976 18315 Z= 0.316 Chirality : 0.037 0.218 2137 Planarity : 0.003 0.042 2331 Dihedral : 3.631 29.961 1809 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.55 % Allowed : 20.18 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.22), residues: 1627 helix: 1.47 (0.16), residues: 1231 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 88 PHE 0.011 0.001 PHE A 181 TYR 0.022 0.001 TYR C 101 ARG 0.015 0.000 ARG Q 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.18 seconds wall clock time: 52 minutes 6.72 seconds (3126.72 seconds total)