Starting phenix.real_space_refine on Fri Oct 30 15:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xtd_67202/10_2026/9xtd_67202.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xtd_67202/10_2026/9xtd_67202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xtd_67202/10_2026/9xtd_67202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xtd_67202/10_2026/9xtd_67202.map" model { file = "/net/cci-nas-00/data/ceres_data/9xtd_67202/10_2026/9xtd_67202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xtd_67202/10_2026/9xtd_67202.cif" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.068 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: 6 Type Number sf(0) Gaussians P 1128 5.49 5 Mg 39 5.21 5 S 47 5.16 5 C 17913 2.51 5 N 6624 2.21 5 O 11756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37507 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 24236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 24236 Classifications: {'RNA': 1127, 'RNAv2': 1} Modifications used: {'rna2p_pur': 84, 'rna2p_pyr': 57, 'rna3p': 5, 'rna3p_pur': 563, 'rna3p_pyr': 419} Link IDs: {'rna2p': 141, 'rna3p': 986} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1716, 1716 Unusual residues: {' MG': 39} Classifications: {'undetermined': 39, 'water': 1677} Link IDs: {None: 1715} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "T" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 7.54, per 1000 atoms: 0.20 Number of scatterers: 37507 At special positions: 0 Unit cell: (132.902, 172.6, 203.668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 1128 15.00 Mg 39 11.99 O 11756 8.00 N 6624 7.00 C 17913 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: 3.40 Conformation dependent library (CDL) restraints added in 713.1 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 44.9% alpha, 20.9% beta 389 base pairs and 613 stacking pairs defined. Time for finding SS restraints: 5.57 Creating SS restraints... Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.213A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.866A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 196 through 206 Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 17 through 32 removed outlier: 4.242A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.605A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 4.385A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 47 through 50 removed outlier: 3.974A pdb=" N GLY K 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 54 through 57 Processing helix chain 'K' and resid 58 through 74 removed outlier: 3.502A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 102 removed outlier: 4.104A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.123A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.084A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 33 No H-bonds generated for 'chain 'R' and resid 31 through 33' Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.538A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 86 removed outlier: 3.540A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.673A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.612A pdb=" N GLN B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 removed outlier: 3.756A pdb=" N ASP B 127 " --> pdb=" O GLY B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 206 through 227 Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.771A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.102A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.487A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 38 through 45 removed outlier: 5.537A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.725A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AA7, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.567A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.567A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 42 through 45 removed outlier: 4.187A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE K 33 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL K 31 " --> pdb=" O ALA K 44 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU K 81 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE K 109 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL K 83 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP K 111 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL K 85 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 29 through 40 removed outlier: 6.578A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL L 93 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR L 64 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.372A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 8 through 17 removed outlier: 7.846A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.999A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 973 hydrogen bonds 1526 hydrogen bond angles 0 basepair planarities 389 basepair parallelities 613 stacking parallelities Total time for adding SS restraints: 35.43 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4220 1.32 - 1.45: 16394 1.45 - 1.57: 15718 1.57 - 1.69: 2251 1.69 - 1.81: 83 Bond restraints: 38666 Sorted by residual: bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.467 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.394 1.473 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C5 MA6 A1518 " pdb=" C4 MA6 A1518 " ideal model delta sigma weight residual 1.394 1.472 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C8 G A 108 " pdb=" N7 G A 108 " ideal model delta sigma weight residual 1.305 1.284 0.021 6.00e-03 2.78e+04 1.22e+01 bond pdb=" N GLN T 55 " pdb=" CA GLN T 55 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.21e+01 ... (remaining 38661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 57209 2.74 - 5.49: 561 5.49 - 8.23: 29 8.23 - 10.98: 9 10.98 - 13.72: 2 Bond angle restraints: 57810 Sorted by residual: angle pdb=" O4' G A 108 " pdb=" C1' G A 108 " pdb=" N9 G A 108 " ideal model delta sigma weight residual 108.50 104.41 4.09 7.00e-01 2.04e+00 3.41e+01 angle pdb=" O5' C A1479 " pdb=" C5' C A1479 " pdb=" C4' C A1479 " ideal model delta sigma weight residual 109.40 113.99 -4.59 8.00e-01 1.56e+00 3.29e+01 angle pdb=" O5' A A 320 " pdb=" C5' A A 320 " pdb=" C4' A A 320 " ideal model delta sigma weight residual 109.40 113.39 -3.99 8.00e-01 1.56e+00 2.48e+01 angle pdb=" N1 C A 841 " pdb=" C2 C A 841 " pdb=" O2 C A 841 " ideal model delta sigma weight residual 118.90 121.84 -2.94 6.00e-01 2.78e+00 2.39e+01 angle pdb=" O4' A A 496 " pdb=" C1' A A 496 " pdb=" N9 A A 496 " ideal model delta sigma weight residual 108.50 111.83 -3.33 7.00e-01 2.04e+00 2.27e+01 ... (remaining 57805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 21256 27.89 - 55.78: 1957 55.78 - 83.67: 1577 83.67 - 111.56: 24 111.56 - 139.45: 6 Dihedral angle restraints: 24820 sinusoidal: 20662 harmonic: 4158 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 60.55 139.45 1 1.50e+01 4.44e-03 7.51e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 66.89 133.11 1 1.50e+01 4.44e-03 7.18e+01 dihedral pdb=" O4' G A 926 " pdb=" C1' G A 926 " pdb=" N9 G A 926 " pdb=" C4 G A 926 " ideal model delta sinusoidal sigma weight residual 68.00 137.89 -69.89 1 1.70e+01 3.46e-03 2.18e+01 ... (remaining 24817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 6161 0.098 - 0.196: 1191 0.196 - 0.293: 16 0.293 - 0.391: 0 0.391 - 0.489: 2 Chirality restraints: 7370 Sorted by residual: chirality pdb=" P C A 528 " pdb=" OP1 C A 528 " pdb=" OP2 C A 528 " pdb=" O5' C A 528 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" P C A 526 " pdb=" OP1 C A 526 " pdb=" OP2 C A 526 " pdb=" O5' C A 526 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C2' PSU A 516 " pdb=" C3' PSU A 516 " pdb=" O2' PSU A 516 " pdb=" C1' PSU A 516 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 7367 not shown) Planarity restraints: 3137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " -0.125 2.00e-02 2.50e+03 2.05e-01 4.19e+02 pdb=" N6 MA6 A1519 " 0.355 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " -0.117 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " -0.123 2.00e-02 2.50e+03 2.05e-01 4.19e+02 pdb=" N6 MA6 A1518 " 0.354 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " -0.116 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " -0.046 2.00e-02 2.50e+03 7.64e-02 1.90e+02 pdb=" N9 2MG A1516 " 0.000 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " 0.037 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " 0.051 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " 0.015 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " 0.007 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " 0.040 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " -0.035 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " -0.074 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " -0.110 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " -0.065 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " -0.028 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " 0.210 2.00e-02 2.50e+03 ... (remaining 3134 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 360 2.43 - 3.04: 22527 3.04 - 3.66: 76036 3.66 - 4.28: 116792 4.28 - 4.90: 151666 Nonbonded interactions: 367381 Sorted by model distance: nonbonded pdb="MG MG A1638 " pdb=" O HOH A2233 " model vdw 1.808 2.170 nonbonded pdb="MG MG A1604 " pdb=" O HOH A2094 " model vdw 1.856 2.170 nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1632 " model vdw 1.870 2.170 nonbonded pdb="MG MG A1613 " pdb=" O HOH A1861 " model vdw 1.889 2.170 nonbonded pdb=" OP2 G A 117 " pdb="MG MG A1632 " model vdw 1.901 2.170 ... (remaining 367376 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 63.610 Find NCS groups from input model: 0.170 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.005 0.085 38666 Z= 0.433 Angle : 0.834 13.724 57810 Z= 0.679 Chirality : 0.061 0.489 7370 Planarity : 0.007 0.205 3137 Dihedral : 22.675 139.449 22136 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1425 helix: 1.35 (0.21), residues: 587 sheet: -0.38 (0.34), residues: 243 loop : -0.18 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 25 TYR 0.016 0.002 TYR L 95 PHE 0.015 0.001 PHE H 49 TRP 0.011 0.001 TRP P 60 HIS 0.003 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.43 (38666) covalent geometry : angle 0.83402 / 0.68 (57810) hydrogen bonds : bond 0.09567 / 10.53 ( 1557) hydrogen bonds : angle 4.50819 / 5.78 ( 3203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 PHE cc_start: 0.8373 (m-80) cc_final: 0.8157 (m-80) outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 0.9002 time to fit residues: 256.2429 Evaluate side-chains 194 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 60.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.2980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 GLN D 54 GLN E 61 GLN E 70 ASN E 73 ASN E 78 ASN E 97 GLN H 18 GLN K 14 GLN O 37 ASN P 9 HIS T 82 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.180519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136218 restraints weight = 31569.222| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.08 r_work: 0.2957 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 38666 Z= 0.340 Angle : 0.784 9.524 57810 Z= 0.415 Chirality : 0.051 0.355 7370 Planarity : 0.007 0.053 3137 Dihedral : 23.457 140.846 19301 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 11.65 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1425 helix: 1.08 (0.21), residues: 586 sheet: -0.50 (0.33), residues: 251 loop : -0.19 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 114 TYR 0.026 0.003 TYR L 117 PHE 0.019 0.002 PHE F 8 TRP 0.015 0.002 TRP P 60 HIS 0.005 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.34 (38666) covalent geometry : angle 0.78444 / 0.42 (57810) hydrogen bonds : bond 0.07908 / 8.50 ( 1557) hydrogen bonds : angle 3.92688 / 5.12 ( 3203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 192 SER cc_start: 0.8018 (m) cc_final: 0.7711 (t) REVERT: E 25 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7244 (m) REVERT: E 31 PHE cc_start: 0.8802 (m-80) cc_final: 0.8574 (m-80) REVERT: E 68 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7685 (mtt180) REVERT: E 147 MET cc_start: 0.8639 (ttp) cc_final: 0.8427 (ttp) REVERT: F 90 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6787 (mtt) REVERT: H 40 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (mp) REVERT: O 26 GLU cc_start: 0.8152 (mp0) cc_final: 0.7901 (mp0) REVERT: B 24 ASN cc_start: 0.7772 (t0) cc_final: 0.7453 (t0) REVERT: B 44 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 100 MET cc_start: 0.7518 (mtp) cc_final: 0.5151 (tmm) outliers start: 30 outliers final: 11 residues processed: 215 average time/residue: 0.9121 time to fit residues: 227.8441 Evaluate side-chains 201 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [140, 115, 210, 178, 169, 131, 215, 27, 98, 203, 65] chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 169 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 60.0000 chunk 203 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 GLN E 73 ASN E 78 ASN E 97 GLN E 148 ASN O 37 ASN O 62 GLN T 82 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.183654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139068 restraints weight = 31801.922| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.16 r_work: 0.2967 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 38666 Z= 0.144 Angle : 0.525 7.371 57810 Z= 0.306 Chirality : 0.037 0.296 7370 Planarity : 0.004 0.039 3137 Dihedral : 23.279 141.094 19301 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.10 % Allowed : 13.08 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1425 helix: 1.27 (0.21), residues: 586 sheet: -0.36 (0.34), residues: 237 loop : -0.20 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 7 TYR 0.018 0.001 TYR L 117 PHE 0.013 0.001 PHE F 8 TRP 0.012 0.001 TRP P 60 HIS 0.004 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (38666) covalent geometry : angle 0.52549 / 0.31 (57810) hydrogen bonds : bond 0.06413 / 6.94 ( 1557) hydrogen bonds : angle 3.60000 / 4.68 ( 3203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 108 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7906 (mppt) REVERT: B 24 ASN cc_start: 0.7637 (t0) cc_final: 0.7253 (t0) REVERT: B 44 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7171 (tm-30) REVERT: B 100 MET cc_start: 0.7485 (mtp) cc_final: 0.5114 (tmm) REVERT: B 203 ASN cc_start: 0.6250 (t0) cc_final: 0.6005 (m-40) outliers start: 25 outliers final: 9 residues processed: 199 average time/residue: 0.9286 time to fit residues: 214.9643 Evaluate side-chains 192 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [52, 205, 115, 38, 114, 150, 13, 98, 71, 103, 158] chunk 52 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 98 optimal weight: 60.0000 chunk 71 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 ASN E 73 ASN E 78 ASN E 97 GLN O 62 GLN T 82 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134353 restraints weight = 31322.652| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.20 r_work: 0.2937 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 38666 Z= 0.370 Angle : 0.823 10.599 57810 Z= 0.429 Chirality : 0.052 0.337 7370 Planarity : 0.007 0.068 3137 Dihedral : 23.424 140.376 19297 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.10 % Allowed : 14.84 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1425 helix: 0.93 (0.21), residues: 585 sheet: -0.44 (0.33), residues: 258 loop : -0.23 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 114 TYR 0.027 0.003 TYR L 117 PHE 0.015 0.002 PHE Q 37 TRP 0.015 0.002 TRP P 60 HIS 0.006 0.002 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.37 (38666) covalent geometry : angle 0.82269 / 0.43 (57810) hydrogen bonds : bond 0.07987 / 8.59 ( 1557) hydrogen bonds : angle 3.82223 / 4.96 ( 3203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7331 (m) REVERT: E 31 PHE cc_start: 0.8842 (m-80) cc_final: 0.8628 (m-80) REVERT: F 90 MET cc_start: 0.7019 (ptp) cc_final: 0.6797 (mtt) REVERT: L 108 LYS cc_start: 0.8260 (mppt) cc_final: 0.7919 (mppt) REVERT: B 24 ASN cc_start: 0.7655 (t0) cc_final: 0.7237 (t0) REVERT: B 42 ASN cc_start: 0.6799 (t0) cc_final: 0.6571 (m-40) REVERT: B 44 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 100 MET cc_start: 0.7545 (mtp) cc_final: 0.5266 (tmm) REVERT: B 194 ASP cc_start: 0.7583 (m-30) cc_final: 0.7358 (m-30) outliers start: 25 outliers final: 17 residues processed: 216 average time/residue: 0.8875 time to fit residues: 223.6860 Evaluate side-chains 215 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [198, 42, 146, 102, 17, 15, 20, 98, 45, 5, 147] chunk 198 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 102 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 98 optimal weight: 60.0000 chunk 45 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN E 70 ASN E 73 ASN E 78 ASN E 97 GLN E 148 ASN O 37 ASN O 62 GLN T 82 GLN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135153 restraints weight = 31261.642| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.11 r_work: 0.2934 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 38666 Z= 0.421 Angle : 0.898 12.301 57810 Z= 0.461 Chirality : 0.056 0.357 7370 Planarity : 0.008 0.079 3137 Dihedral : 23.436 140.217 19297 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.10 % Allowed : 14.59 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.22), residues: 1425 helix: 0.55 (0.20), residues: 592 sheet: -0.38 (0.33), residues: 254 loop : -0.39 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 114 TYR 0.031 0.004 TYR L 117 PHE 0.016 0.002 PHE Q 37 TRP 0.017 0.003 TRP P 60 HIS 0.008 0.002 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.42 (38666) covalent geometry : angle 0.89768 / 0.46 (57810) hydrogen bonds : bond 0.08541 / 9.22 ( 1557) hydrogen bonds : angle 3.97614 / 5.18 ( 3203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 SER cc_start: 0.8703 (p) cc_final: 0.8470 (p) REVERT: D 155 VAL cc_start: 0.8075 (p) cc_final: 0.7762 (t) REVERT: E 25 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7524 (m) REVERT: E 31 PHE cc_start: 0.8870 (m-80) cc_final: 0.8637 (m-80) REVERT: H 67 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7438 (mm-40) REVERT: L 18 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8251 (ptpt) REVERT: L 94 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8335 (mtt180) REVERT: L 108 LYS cc_start: 0.8201 (mppt) cc_final: 0.7892 (mppt) REVERT: Q 63 GLU cc_start: 0.8705 (tt0) cc_final: 0.8404 (tt0) REVERT: B 9 MET cc_start: 0.8198 (mmp) cc_final: 0.7928 (mmt) REVERT: B 44 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7138 (tm-30) REVERT: B 100 MET cc_start: 0.7403 (mtp) cc_final: 0.5398 (tmm) REVERT: B 175 GLU cc_start: 0.7468 (tt0) cc_final: 0.7208 (mt-10) outliers start: 37 outliers final: 19 residues processed: 225 average time/residue: 0.8905 time to fit residues: 234.1222 Evaluate side-chains 217 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [19, 87, 213, 134, 124, 18, 112, 178, 233, 57, 119] chunk 19 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 178 optimal weight: 50.0000 chunk 233 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 61 GLN E 70 ASN E 73 ASN E 78 ASN E 97 GLN E 148 ASN O 37 ASN O 62 GLN P 63 GLN T 82 GLN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 178 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134342 restraints weight = 31449.742| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.23 r_work: 0.2901 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 38666 Z= 0.165 Angle : 0.568 8.671 57810 Z= 0.324 Chirality : 0.039 0.272 7370 Planarity : 0.005 0.043 3137 Dihedral : 23.235 140.708 19297 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.26 % Allowed : 16.01 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1425 helix: 1.03 (0.21), residues: 592 sheet: -0.25 (0.34), residues: 246 loop : -0.22 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 112 TYR 0.022 0.002 TYR L 117 PHE 0.015 0.002 PHE F 8 TRP 0.015 0.001 TRP B 104 HIS 0.006 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.17 (38666) covalent geometry : angle 0.56809 / 0.32 (57810) hydrogen bonds : bond 0.06716 / 7.25 ( 1557) hydrogen bonds : angle 3.64835 / 4.75 ( 3203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.566 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: D 144 SER cc_start: 0.8718 (p) cc_final: 0.8499 (p) REVERT: D 155 VAL cc_start: 0.8014 (p) cc_final: 0.7616 (t) REVERT: E 148 ASN cc_start: 0.8393 (m-40) cc_final: 0.8192 (m110) REVERT: K 22 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7772 (pp) REVERT: L 94 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8311 (mtt180) REVERT: L 103 ASP cc_start: 0.8899 (m-30) cc_final: 0.8600 (m-30) REVERT: L 108 LYS cc_start: 0.8158 (mppt) cc_final: 0.7880 (mppt) REVERT: B 44 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7097 (tm-30) REVERT: B 78 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: B 100 MET cc_start: 0.7372 (mtp) cc_final: 0.5304 (tmm) REVERT: B 175 GLU cc_start: 0.7339 (tt0) cc_final: 0.7030 (mt-10) outliers start: 27 outliers final: 13 residues processed: 205 average time/residue: 0.8792 time to fit residues: 210.2187 Evaluate side-chains 201 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [149, 208, 69, 162, 194, 105, 14, 235, 84, 198, 25] chunk 149 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 69 optimal weight: 50.0000 chunk 162 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 84 optimal weight: 50.0000 chunk 198 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 ASN E 73 ASN E 78 ASN E 97 GLN O 37 ASN O 62 GLN T 82 GLN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 178 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132313 restraints weight = 31229.443| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.17 r_work: 0.2908 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 38666 Z= 0.425 Angle : 0.898 11.911 57810 Z= 0.459 Chirality : 0.056 0.301 7370 Planarity : 0.008 0.071 3137 Dihedral : 23.377 140.192 19297 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 16.18 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1425 helix: 0.71 (0.20), residues: 592 sheet: -0.38 (0.33), residues: 259 loop : -0.28 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 114 TYR 0.030 0.003 TYR L 117 PHE 0.017 0.002 PHE Q 37 TRP 0.017 0.003 TRP P 60 HIS 0.008 0.002 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.42 (38666) covalent geometry : angle 0.89815 / 0.46 (57810) hydrogen bonds : bond 0.08292 / 8.92 ( 1557) hydrogen bonds : angle 3.89231 / 5.03 ( 3203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7523 (m110) REVERT: D 144 SER cc_start: 0.8731 (p) cc_final: 0.8505 (p) REVERT: D 155 VAL cc_start: 0.8100 (p) cc_final: 0.7801 (t) REVERT: L 94 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8337 (mtt180) REVERT: L 108 LYS cc_start: 0.8271 (mppt) cc_final: 0.7952 (mppt) REVERT: P 8 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8721 (ttt90) REVERT: Q 63 GLU cc_start: 0.8652 (tt0) cc_final: 0.8450 (tt0) REVERT: B 44 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7072 (tm-30) REVERT: B 100 MET cc_start: 0.7479 (mtp) cc_final: 0.5467 (tmm) REVERT: B 175 GLU cc_start: 0.7603 (tt0) cc_final: 0.7235 (mt-10) outliers start: 30 outliers final: 19 residues processed: 212 average time/residue: 0.9211 time to fit residues: 227.5059 Evaluate side-chains 211 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [100, 174, 118, 120, 104, 40, 204, 52, 137, 72, 195] chunk 100 optimal weight: 50.0000 chunk 174 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 ASN E 73 ASN E 78 ASN E 97 GLN E 148 ASN O 37 ASN O 62 GLN T 82 GLN B 24 ASN B 178 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135277 restraints weight = 31313.611| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.21 r_work: 0.2914 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 38666 Z= 0.162 Angle : 0.556 10.212 57810 Z= 0.318 Chirality : 0.038 0.270 7370 Planarity : 0.005 0.046 3137 Dihedral : 23.182 140.951 19297 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.01 % Allowed : 16.76 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1425 helix: 1.10 (0.21), residues: 592 sheet: -0.27 (0.33), residues: 257 loop : -0.15 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 112 TYR 0.020 0.002 TYR L 117 PHE 0.015 0.001 PHE F 8 TRP 0.018 0.002 TRP B 104 HIS 0.005 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (38666) covalent geometry : angle 0.55566 / 0.32 (57810) hydrogen bonds : bond 0.06579 / 7.11 ( 1557) hydrogen bonds : angle 3.60864 / 4.67 ( 3203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.791 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: D 144 SER cc_start: 0.8693 (p) cc_final: 0.8470 (p) REVERT: D 155 VAL cc_start: 0.7989 (p) cc_final: 0.7599 (t) REVERT: E 14 LYS cc_start: 0.8851 (mtpm) cc_final: 0.8623 (mtpt) REVERT: F 90 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6765 (mtt) REVERT: L 94 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8319 (mtt180) REVERT: L 103 ASP cc_start: 0.8880 (m-30) cc_final: 0.8567 (m-30) REVERT: L 108 LYS cc_start: 0.8120 (mppt) cc_final: 0.7843 (mppt) REVERT: B 44 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7301 (tm-30) REVERT: B 100 MET cc_start: 0.7370 (mtp) cc_final: 0.5375 (tmm) REVERT: B 175 GLU cc_start: 0.7253 (tt0) cc_final: 0.6984 (mt-10) outliers start: 24 outliers final: 13 residues processed: 200 average time/residue: 0.9296 time to fit residues: 215.8744 Evaluate side-chains 199 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [128, 24, 220, 89, 5, 168, 176, 133, 248, 219, 204] chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 ASN E 78 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN O 62 GLN T 82 GLN B 24 ASN B 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.178854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133904 restraints weight = 31267.496| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.06 r_work: 0.2941 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 38666 Z= 0.319 Angle : 0.759 9.972 57810 Z= 0.401 Chirality : 0.049 0.295 7370 Planarity : 0.006 0.058 3137 Dihedral : 23.285 140.579 19297 Min Nonbonded Distance : 1.562 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.10 % Allowed : 17.10 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1425 helix: 0.90 (0.21), residues: 592 sheet: -0.36 (0.32), residues: 265 loop : -0.18 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 114 TYR 0.026 0.003 TYR L 117 PHE 0.015 0.002 PHE Q 37 TRP 0.015 0.002 TRP P 60 HIS 0.007 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.32 (38666) covalent geometry : angle 0.75908 / 0.40 (57810) hydrogen bonds : bond 0.07614 / 8.18 ( 1557) hydrogen bonds : angle 3.75570 / 4.83 ( 3203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.645 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: D 144 SER cc_start: 0.8702 (p) cc_final: 0.8472 (p) REVERT: D 155 VAL cc_start: 0.8043 (p) cc_final: 0.7731 (t) REVERT: E 14 LYS cc_start: 0.8869 (mtpm) cc_final: 0.8660 (mtpt) REVERT: F 90 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6865 (mtt) REVERT: L 94 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8302 (mtt180) REVERT: L 108 LYS cc_start: 0.8183 (mppt) cc_final: 0.7905 (mppt) REVERT: B 36 ASN cc_start: 0.6879 (t0) cc_final: 0.6481 (t0) REVERT: B 44 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 100 MET cc_start: 0.7314 (mtp) cc_final: 0.5431 (tmm) REVERT: B 175 GLU cc_start: 0.7612 (tt0) cc_final: 0.7210 (mt-10) REVERT: B 203 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6780 (m-40) outliers start: 25 outliers final: 17 residues processed: 207 average time/residue: 0.9356 time to fit residues: 225.0875 Evaluate side-chains 211 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 203 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [241, 95, 39, 148, 212, 226, 18, 34, 205, 69, 170] chunk 241 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 69 optimal weight: 50.0000 chunk 170 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 ASN E 73 ASN E 78 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN O 62 GLN T 82 GLN B 24 ASN B 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133121 restraints weight = 31241.849| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.19 r_work: 0.2871 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38666 Z= 0.256 Angle : 0.677 12.521 57810 Z= 0.366 Chirality : 0.044 0.285 7370 Planarity : 0.006 0.054 3137 Dihedral : 23.231 140.272 19297 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.18 % Allowed : 17.27 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1425 helix: 0.97 (0.21), residues: 591 sheet: -0.22 (0.33), residues: 257 loop : -0.22 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 112 TYR 0.025 0.002 TYR L 95 PHE 0.022 0.002 PHE B 50 TRP 0.016 0.002 TRP B 104 HIS 0.006 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.26 (38666) covalent geometry : angle 0.67676 / 0.37 (57810) hydrogen bonds : bond 0.07131 / 7.67 ( 1557) hydrogen bonds : angle 3.68360 / 4.76 ( 3203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.844 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: D 89 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7420 (m110) REVERT: D 144 SER cc_start: 0.8709 (p) cc_final: 0.8481 (p) REVERT: D 155 VAL cc_start: 0.7944 (p) cc_final: 0.7601 (t) REVERT: L 94 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8315 (mtt180) REVERT: L 108 LYS cc_start: 0.8186 (mppt) cc_final: 0.7875 (mppt) REVERT: B 36 ASN cc_start: 0.6918 (t0) cc_final: 0.6449 (t0) REVERT: B 44 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 100 MET cc_start: 0.7366 (mtp) cc_final: 0.5351 (tmm) REVERT: B 175 GLU cc_start: 0.7335 (tt0) cc_final: 0.7004 (mt-10) REVERT: B 203 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6725 (m-40) outliers start: 26 outliers final: 18 residues processed: 205 average time/residue: 0.9384 time to fit residues: 222.9982 Evaluate side-chains 209 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 203 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [123, 97, 245, 40, 149, 222, 238, 75, 241, 121, 46] chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 245 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 61 GLN E 70 ASN E 73 ASN E 78 ASN E 97 GLN K 63 GLN O 37 ASN O 62 GLN T 82 GLN B 24 ASN B 89 GLN B 178 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.179460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133701 restraints weight = 31195.484| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.09 r_work: 0.2918 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 38666 Z= 0.252 Angle : 0.679 10.294 57810 Z= 0.369 Chirality : 0.045 0.292 7370 Planarity : 0.006 0.055 3137 Dihedral : 23.226 140.785 19297 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.93 % Allowed : 17.35 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.22), residues: 1425 helix: 0.93 (0.21), residues: 591 sheet: -0.19 (0.33), residues: 257 loop : -0.22 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 112 TYR 0.024 0.002 TYR L 95 PHE 0.015 0.002 PHE F 8 TRP 0.015 0.002 TRP B 104 HIS 0.007 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.25 (38666) covalent geometry : angle 0.67930 / 0.37 (57810) hydrogen bonds : bond 0.07215 / 7.75 ( 1557) hydrogen bonds : angle 3.68481 / 4.75 ( 3203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16050.52 seconds wall clock time: 273 minutes 18.19 seconds (16398.19 seconds total)