Starting phenix.real_space_refine on Mon Apr 15 15:23:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/04_2024/7bgd_12178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/04_2024/7bgd_12178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/04_2024/7bgd_12178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/04_2024/7bgd_12178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/04_2024/7bgd_12178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/04_2024/7bgd_12178.pdb" } resolution = 3.2 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1128 5.49 5 S 30 5.16 5 C 17806 2.51 5 N 6522 2.21 5 O 9878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 83": "OE1" <-> "OE2" Residue "b GLU 85": "OE1" <-> "OE2" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 195": "OE1" <-> "OE2" Residue "d ARG 29": "NH1" <-> "NH2" Residue "d GLU 46": "OE1" <-> "OE2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d GLU 184": "OE1" <-> "OE2" Residue "d ARG 200": "NH1" <-> "NH2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e GLU 78": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f GLU 39": "OE1" <-> "OE2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h GLU 117": "OE1" <-> "OE2" Residue "k GLU 37": "OE1" <-> "OE2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "l ARG 49": "NH1" <-> "NH2" Residue "l ARG 107": "NH1" <-> "NH2" Residue "l ARG 127": "NH1" <-> "NH2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p ARG 26": "NH1" <-> "NH2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "q TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 76": "NH1" <-> "NH2" Residue "r ARG 10": "NH1" <-> "NH2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r GLU 32": "OE1" <-> "OE2" Residue "t GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35364 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 693 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 14, 'rna3p': 17} Chain: "a" Number of atoms: 23497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 23497 Classifications: {'RNA': 1096} Modifications used: {'rna2p_pur': 81, 'rna2p_pyr': 59, 'rna3p_pur': 542, 'rna3p_pyr': 414} Link IDs: {'rna2p': 140, 'rna3p': 955} Chain breaks: 1 Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1299 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain breaks: 2 Chain: "d" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1595 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain breaks: 1 Chain: "e" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1169 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "f" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 798 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "k" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Time building chain proxies: 19.37, per 1000 atoms: 0.55 Number of scatterers: 35364 At special positions: 0 Unit cell: (145.18, 183.26, 172.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 1128 15.00 O 9878 8.00 N 6522 7.00 C 17806 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 - 3.50 Amino acid : False - 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: 17.77 Conformation dependent library (CDL) restraints added in 2.7 seconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 14 sheets defined 34.7% alpha, 17.7% beta 359 base pairs and 687 stacking pairs defined. Time for finding SS restraints: 15.76 Creating SS restraints... Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 43 through 60 Processing helix chain 'b' and resid 61 through 63 No H-bonds generated for 'chain 'b' and resid 61 through 63' Processing helix chain 'b' and resid 77 through 82 Processing helix chain 'b' and resid 206 through 223 removed outlier: 3.631A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA b 218 " --> pdb=" O THR b 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 14 removed outlier: 3.633A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.597A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 Processing helix chain 'd' and resid 81 through 91 removed outlier: 3.604A pdb=" N ALA d 91 " --> pdb=" O MET d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 116 Processing helix chain 'd' and resid 142 through 146 removed outlier: 4.203A pdb=" N GLN d 146 " --> pdb=" O GLU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 157 removed outlier: 3.751A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 196 removed outlier: 3.575A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 109 through 116 removed outlier: 3.668A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 15 through 30 removed outlier: 3.512A pdb=" N LYS f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA f 21 " --> pdb=" O ASP f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 83 removed outlier: 3.785A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE f 82 " --> pdb=" O ARG f 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.811A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 96 through 101 Processing helix chain 'h' and resid 114 through 121 removed outlier: 3.766A pdb=" N ARG h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.792A pdb=" N LEU k 50 " --> pdb=" O ALA k 47 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY k 51 " --> pdb=" O GLY k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 57 removed outlier: 3.667A pdb=" N LYS k 57 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.771A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.812A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'o' and resid 4 through 12 Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.621A pdb=" N ARG o 44 " --> pdb=" O ASN o 40 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 74 removed outlier: 4.021A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.571A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 63 removed outlier: 3.569A pdb=" N ASP p 63 " --> pdb=" O LYS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 78 Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.517A pdb=" N LYS p 83 " --> pdb=" O GLY p 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 35 removed outlier: 3.644A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 Processing helix chain 't' and resid 8 through 38 removed outlier: 3.849A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA t 27 " --> pdb=" O SER t 23 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 63 removed outlier: 3.797A pdb=" N LEU t 49 " --> pdb=" O ASN t 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER t 51 " --> pdb=" O ASN t 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS t 55 " --> pdb=" O SER t 51 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL t 57 " --> pdb=" O ALA t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 79 Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 35 removed outlier: 4.087A pdb=" N THR b 33 " --> pdb=" O ILE b 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE b 38 " --> pdb=" O ARG b 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 90 through 91 removed outlier: 3.936A pdb=" N PHE b 69 " --> pdb=" O PHE b 90 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'd' and resid 124 through 126 removed outlier: 3.946A pdb=" N VAL d 126 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE d 119 " --> pdb=" O VAL d 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.017A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 85 through 87 removed outlier: 6.369A pdb=" N ILE e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER e 127 " --> pdb=" O ILE e 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.653A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.653A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 24 through 26 removed outlier: 3.745A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 76 through 79 Processing sheet with id=AB1, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.944A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 41 through 45 removed outlier: 6.550A pdb=" N GLY k 19 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 92 through 95 removed outlier: 6.864A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL l 50 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR l 65 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR l 108 " --> pdb=" O ASN l 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 5 through 11 removed outlier: 6.319A pdb=" N ASN p 41 " --> pdb=" O PRO p 16 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE p 20 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 41 through 48 removed outlier: 3.571A pdb=" N TYR q 42 " --> pdb=" O THR q 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 29 " --> pdb=" O TYR q 42 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU q 28 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 13.031A pdb=" N TYR q 30 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 16.569A pdb=" N VAL q 9 " --> pdb=" O TYR q 30 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 894 hydrogen bonds 1446 hydrogen bond angles 0 basepair planarities 359 basepair parallelities 687 stacking parallelities Total time for adding SS restraints: 26.49 Time building geometry restraints manager: 19.24 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: 4586 1.32 - 1.45: 16148 1.45 - 1.57: 15375 1.57 - 1.69: 2254 1.69 - 1.81: 56 Bond restraints: 38419 Sorted by residual: bond pdb=" C SER l 118 " pdb=" N GLY l 119 " ideal model delta sigma weight residual 1.330 1.440 -0.110 8.80e-03 1.29e+04 1.55e+02 bond pdb=" C THR l 117 " pdb=" N SER l 118 " ideal model delta sigma weight residual 1.330 1.487 -0.157 1.45e-02 4.76e+03 1.17e+02 bond pdb=" C PHE b 90 " pdb=" N TYR b 91 " ideal model delta sigma weight residual 1.330 1.455 -0.125 1.47e-02 4.63e+03 7.18e+01 bond pdb=" C TYR b 91 " pdb=" N ILE b 92 " ideal model delta sigma weight residual 1.332 1.420 -0.088 1.36e-02 5.41e+03 4.18e+01 bond pdb=" CG1 ILE d 128 " pdb=" CD1 ILE d 128 " ideal model delta sigma weight residual 1.513 1.365 0.148 3.90e-02 6.57e+02 1.45e+01 ... (remaining 38414 not shown) Histogram of bond angle deviations from ideal: 96.99 - 105.21: 5662 105.21 - 113.43: 22748 113.43 - 121.64: 19513 121.64 - 129.86: 8756 129.86 - 138.08: 772 Bond angle restraints: 57451 Sorted by residual: angle pdb=" C SER l 118 " pdb=" N GLY l 119 " pdb=" CA GLY l 119 " ideal model delta sigma weight residual 119.92 129.97 -10.05 9.60e-01 1.09e+00 1.10e+02 angle pdb=" CA PHE b 90 " pdb=" C PHE b 90 " pdb=" N TYR b 91 " ideal model delta sigma weight residual 116.45 106.52 9.93 1.23e+00 6.61e-01 6.52e+01 angle pdb=" N SER l 128 " pdb=" CA SER l 128 " pdb=" C SER l 128 " ideal model delta sigma weight residual 111.14 102.70 8.44 1.08e+00 8.57e-01 6.10e+01 angle pdb=" O SER l 118 " pdb=" C SER l 118 " pdb=" N GLY l 119 " ideal model delta sigma weight residual 123.16 114.44 8.72 1.16e+00 7.43e-01 5.65e+01 angle pdb=" C3' A a 540 " pdb=" O3' A a 540 " pdb=" P A a 541 " ideal model delta sigma weight residual 120.20 130.72 -10.52 1.50e+00 4.44e-01 4.92e+01 ... (remaining 57446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 21510 35.22 - 70.43: 2698 70.43 - 105.65: 307 105.65 - 140.86: 6 140.86 - 176.08: 12 Dihedral angle restraints: 24533 sinusoidal: 20479 harmonic: 4054 Sorted by residual: dihedral pdb=" O4' U a 477 " pdb=" C1' U a 477 " pdb=" N1 U a 477 " pdb=" C2 U a 477 " ideal model delta sinusoidal sigma weight residual 200.00 23.92 176.08 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U a 315 " pdb=" C1' U a 315 " pdb=" N1 U a 315 " pdb=" C2 U a 315 " ideal model delta sinusoidal sigma weight residual -160.00 11.70 -171.70 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U a 851 " pdb=" C1' U a 851 " pdb=" N1 U a 851 " pdb=" C2 U a 851 " ideal model delta sinusoidal sigma weight residual 200.00 35.92 164.08 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 24530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 6669 0.101 - 0.201: 597 0.201 - 0.302: 63 0.302 - 0.402: 11 0.402 - 0.503: 5 Chirality restraints: 7345 Sorted by residual: chirality pdb=" CB ILE h 127 " pdb=" CA ILE h 127 " pdb=" CG1 ILE h 127 " pdb=" CG2 ILE h 127 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CB VAL d 141 " pdb=" CA VAL d 141 " pdb=" CG1 VAL d 141 " pdb=" CG2 VAL d 141 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C1' A a 61 " pdb=" O4' A a 61 " pdb=" C2' A a 61 " pdb=" N9 A a 61 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 7342 not shown) Planarity restraints: 3085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR b 91 " 0.030 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C TYR b 91 " -0.110 2.00e-02 2.50e+03 pdb=" O TYR b 91 " 0.045 2.00e-02 2.50e+03 pdb=" N ILE b 92 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE b 90 " 0.028 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C PHE b 90 " -0.105 2.00e-02 2.50e+03 pdb=" O PHE b 90 " 0.044 2.00e-02 2.50e+03 pdb=" N TYR b 91 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY l 119 " 0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C GLY l 119 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY l 119 " 0.040 2.00e-02 2.50e+03 pdb=" N VAL l 120 " 0.033 2.00e-02 2.50e+03 ... (remaining 3082 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10539 2.84 - 3.36: 26884 3.36 - 3.87: 80066 3.87 - 4.39: 89718 4.39 - 4.90: 119146 Nonbonded interactions: 326353 Sorted by model distance: nonbonded pdb=" OP1 A a 212 " pdb=" O2' C a 229 " model vdw 2.327 2.440 nonbonded pdb=" O2' G a 262 " pdb=" O ASP q 20 " model vdw 2.329 2.440 nonbonded pdb=" O2' G a 900 " pdb=" O6 G a 916 " model vdw 2.331 2.440 nonbonded pdb=" OP1 U a 383 " pdb=" OG1 THR p 70 " model vdw 2.334 2.440 nonbonded pdb=" O ILE o 29 " pdb=" OG1 THR o 33 " model vdw 2.336 2.440 ... (remaining 326348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.160 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 116.390 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:0.010 Internal consistency checks: 0.000 Total: 127.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.008 0.157 38419 Z= 0.487 Angle : 1.300 20.379 57451 Z= 0.629 Chirality : 0.062 0.503 7345 Planarity : 0.009 0.102 3085 Dihedral : 23.454 176.081 21917 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.97 % Favored : 91.74 % Rotamer: Outliers : 2.16 % Allowed : 10.70 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.26 (0.16), residues: 1380 helix: -4.32 (0.10), residues: 475 sheet: -2.84 (0.30), residues: 229 loop : -3.02 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP b 96 HIS 0.048 0.004 HIS k 118 PHE 0.025 0.003 PHE e 31 TYR 0.032 0.004 TYR q 30 ARG 0.011 0.001 ARG l 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 409 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7837 (tp40) cc_final: 0.7537 (mm-40) REVERT: b 73 LYS cc_start: 0.7724 (tptt) cc_final: 0.7522 (tptm) REVERT: b 77 GLN cc_start: 0.7228 (pt0) cc_final: 0.6675 (pm20) REVERT: b 188 ASP cc_start: 0.5682 (m-30) cc_final: 0.4890 (t0) REVERT: e 32 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7170 (mtm-85) REVERT: e 88 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7596 (mtt180) REVERT: f 5 GLU cc_start: 0.7090 (tt0) cc_final: 0.6744 (tt0) REVERT: f 70 ASN cc_start: 0.7400 (p0) cc_final: 0.7092 (p0) REVERT: f 74 ASP cc_start: 0.8072 (p0) cc_final: 0.7859 (p0) REVERT: f 79 LEU cc_start: 0.8108 (mm) cc_final: 0.7880 (mt) REVERT: h 21 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7592 (mpt180) REVERT: h 105 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8817 (pp) REVERT: l 25 ASN cc_start: 0.8907 (p0) cc_final: 0.8623 (p0) REVERT: l 53 MET cc_start: 0.8684 (ptm) cc_final: 0.8447 (ptm) REVERT: l 60 SER cc_start: 0.7870 (t) cc_final: 0.7360 (t) REVERT: o 59 MET cc_start: 0.8020 (mtt) cc_final: 0.7782 (mtt) REVERT: p 62 ASN cc_start: 0.8065 (m-40) cc_final: 0.7736 (m110) REVERT: p 77 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8371 (mtmt) REVERT: q 70 SER cc_start: 0.8910 (t) cc_final: 0.8507 (t) outliers start: 26 outliers final: 8 residues processed: 424 average time/residue: 0.5228 time to fit residues: 340.9221 Evaluate side-chains 329 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 320 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 GLN b 66 GLN b 159 GLN b 190 ASN ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN k 18 ASN k 64 GLN k 77 HIS l 5 ASN l 6 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN p 46 ASN p 62 ASN p 87 GLN t 42 ASN t 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 38419 Z= 0.271 Angle : 0.630 12.517 57451 Z= 0.326 Chirality : 0.037 0.286 7345 Planarity : 0.006 0.073 3085 Dihedral : 23.697 178.338 19057 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.06 % Allowed : 18.08 % Favored : 76.87 % 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: -3.60 (0.19), residues: 1380 helix: -2.04 (0.19), residues: 484 sheet: -2.64 (0.30), residues: 237 loop : -2.49 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP k 44 HIS 0.011 0.001 HIS k 118 PHE 0.038 0.002 PHE k 61 TYR 0.017 0.002 TYR r 56 ARG 0.007 0.001 ARG d 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 325 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.7948 (t0) cc_final: 0.7667 (t0) REVERT: b 73 LYS cc_start: 0.7455 (tptt) cc_final: 0.7161 (ttpt) REVERT: b 77 GLN cc_start: 0.7128 (pt0) cc_final: 0.6513 (pm20) REVERT: b 151 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6386 (pp) REVERT: d 119 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (pt) REVERT: e 43 ASN cc_start: 0.7696 (p0) cc_final: 0.7488 (p0) REVERT: e 45 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7963 (mtp-110) REVERT: e 60 ILE cc_start: 0.8540 (pt) cc_final: 0.8222 (mt) REVERT: f 5 GLU cc_start: 0.7206 (tt0) cc_final: 0.6881 (tt0) REVERT: f 60 TYR cc_start: 0.8652 (m-80) cc_final: 0.8255 (m-80) REVERT: f 74 ASP cc_start: 0.8043 (p0) cc_final: 0.7593 (p0) REVERT: f 79 LEU cc_start: 0.8267 (mm) cc_final: 0.8049 (mt) REVERT: h 39 ILE cc_start: 0.9175 (mm) cc_final: 0.8889 (mt) REVERT: h 61 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7894 (ttm110) REVERT: k 24 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7609 (tpt-90) REVERT: k 65 MET cc_start: 0.7733 (mpp) cc_final: 0.7444 (mmt) REVERT: k 125 LYS cc_start: 0.7903 (tmmt) cc_final: 0.7246 (tptm) REVERT: l 60 SER cc_start: 0.7679 (t) cc_final: 0.7136 (t) REVERT: o 59 MET cc_start: 0.8127 (mtt) cc_final: 0.7846 (mtt) REVERT: q 28 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7626 (mm-30) REVERT: r 27 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7455 (t0) REVERT: r 35 LYS cc_start: 0.8556 (mptt) cc_final: 0.8192 (mptt) REVERT: t 24 GLN cc_start: 0.8365 (tt0) cc_final: 0.8160 (tt0) outliers start: 61 outliers final: 44 residues processed: 360 average time/residue: 0.5513 time to fit residues: 309.6530 Evaluate side-chains 349 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 302 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 GLN d 112 GLN d 118 HIS ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 38419 Z= 0.356 Angle : 0.666 12.033 57451 Z= 0.342 Chirality : 0.039 0.288 7345 Planarity : 0.005 0.065 3085 Dihedral : 23.591 176.830 19057 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 7.21 % Allowed : 19.32 % Favored : 73.47 % 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: -2.82 (0.21), residues: 1380 helix: -1.02 (0.22), residues: 490 sheet: -2.40 (0.31), residues: 243 loop : -2.28 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP k 44 HIS 0.012 0.002 HIS o 51 PHE 0.023 0.002 PHE k 61 TYR 0.021 0.002 TYR p 40 ARG 0.006 0.001 ARG l 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 324 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.7955 (t0) cc_final: 0.7618 (t0) REVERT: b 73 LYS cc_start: 0.7401 (tptt) cc_final: 0.7109 (ttpt) REVERT: b 77 GLN cc_start: 0.6955 (pt0) cc_final: 0.6422 (pm20) REVERT: b 151 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6332 (pp) REVERT: d 47 TYR cc_start: 0.9168 (t80) cc_final: 0.8941 (t80) REVERT: d 119 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8371 (pt) REVERT: f 60 TYR cc_start: 0.8688 (m-80) cc_final: 0.8332 (m-80) REVERT: f 79 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8122 (mt) REVERT: h 39 ILE cc_start: 0.9180 (mm) cc_final: 0.8897 (mt) REVERT: h 61 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7703 (ttm170) REVERT: h 98 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8474 (mp) REVERT: k 24 ARG cc_start: 0.8005 (tpt-90) cc_final: 0.7619 (tpt-90) REVERT: k 65 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: k 125 LYS cc_start: 0.8082 (tmmt) cc_final: 0.7380 (tptm) REVERT: l 60 SER cc_start: 0.7726 (t) cc_final: 0.7186 (t) REVERT: o 59 MET cc_start: 0.8081 (mtt) cc_final: 0.7843 (mtt) REVERT: p 74 ILE cc_start: 0.9126 (pt) cc_final: 0.8827 (pt) REVERT: p 88 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7813 (ttmm) REVERT: q 4 ARG cc_start: 0.6918 (tpm170) cc_final: 0.6572 (tpm170) REVERT: q 28 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7645 (mm-30) REVERT: r 27 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7653 (t70) REVERT: r 35 LYS cc_start: 0.8743 (mptt) cc_final: 0.8376 (mptt) outliers start: 87 outliers final: 63 residues processed: 374 average time/residue: 0.5213 time to fit residues: 307.3093 Evaluate side-chains 385 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 316 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 39 GLU Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 31 VAL Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 38419 Z= 0.426 Angle : 0.700 11.815 57451 Z= 0.357 Chirality : 0.042 0.270 7345 Planarity : 0.005 0.068 3085 Dihedral : 23.583 175.879 19057 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.20 % Favored : 90.72 % Rotamer: Outliers : 7.88 % Allowed : 20.48 % Favored : 71.64 % 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: -2.57 (0.21), residues: 1380 helix: -0.77 (0.22), residues: 487 sheet: -2.34 (0.31), residues: 248 loop : -2.13 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP k 44 HIS 0.008 0.002 HIS k 118 PHE 0.020 0.002 PHE k 61 TYR 0.023 0.002 TYR f 8 ARG 0.006 0.001 ARG d 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 313 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7349 (mmm) cc_final: 0.6748 (mmm) REVERT: b 73 LYS cc_start: 0.7448 (tptt) cc_final: 0.7107 (ttpt) REVERT: b 151 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6419 (pp) REVERT: d 47 TYR cc_start: 0.9234 (t80) cc_final: 0.8968 (t80) REVERT: d 119 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8385 (pt) REVERT: e 43 ASN cc_start: 0.7935 (p0) cc_final: 0.7641 (p0) REVERT: f 60 TYR cc_start: 0.8702 (m-80) cc_final: 0.8326 (m-80) REVERT: f 70 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7108 (p0) REVERT: f 74 ASP cc_start: 0.8408 (p0) cc_final: 0.7661 (p0) REVERT: f 79 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8171 (mt) REVERT: h 22 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8058 (m-70) REVERT: h 39 ILE cc_start: 0.9189 (mm) cc_final: 0.8903 (mt) REVERT: h 61 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7722 (ttm170) REVERT: h 98 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8508 (mp) REVERT: k 24 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7640 (tpt-90) REVERT: k 65 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7433 (mmt) REVERT: k 87 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8098 (ttpt) REVERT: k 125 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7372 (tptm) REVERT: l 60 SER cc_start: 0.7895 (t) cc_final: 0.7367 (t) REVERT: l 109 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7475 (p-80) REVERT: o 59 MET cc_start: 0.8090 (mtt) cc_final: 0.7838 (mtt) REVERT: p 74 ILE cc_start: 0.9187 (pt) cc_final: 0.8931 (pt) REVERT: q 4 ARG cc_start: 0.7021 (tpm170) cc_final: 0.6719 (tpm170) REVERT: q 28 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7603 (mm-30) REVERT: r 27 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7548 (t70) REVERT: r 35 LYS cc_start: 0.8832 (mptt) cc_final: 0.8503 (mptt) outliers start: 95 outliers final: 73 residues processed: 371 average time/residue: 0.5278 time to fit residues: 309.1937 Evaluate side-chains 387 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 305 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 70 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 31 VAL Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 38419 Z= 0.219 Angle : 0.578 11.638 57451 Z= 0.298 Chirality : 0.035 0.236 7345 Planarity : 0.004 0.068 3085 Dihedral : 23.515 177.872 19057 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 6.47 % Allowed : 22.55 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.22), residues: 1380 helix: -0.28 (0.23), residues: 482 sheet: -2.23 (0.32), residues: 231 loop : -1.93 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP k 44 HIS 0.010 0.002 HIS k 77 PHE 0.018 0.002 PHE k 61 TYR 0.022 0.002 TYR f 8 ARG 0.006 0.001 ARG q 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.7693 (ptmt) cc_final: 0.7171 (tptm) REVERT: b 151 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6592 (pp) REVERT: e 43 ASN cc_start: 0.7763 (p0) cc_final: 0.7508 (p0) REVERT: f 74 ASP cc_start: 0.8373 (p0) cc_final: 0.7722 (p0) REVERT: f 79 LEU cc_start: 0.8480 (mm) cc_final: 0.7991 (mt) REVERT: h 10 MET cc_start: 0.7864 (ttt) cc_final: 0.7602 (ttt) REVERT: h 39 ILE cc_start: 0.9167 (mm) cc_final: 0.8888 (mt) REVERT: h 61 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7681 (ttm170) REVERT: h 98 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8453 (mp) REVERT: k 24 ARG cc_start: 0.7987 (tpt-90) cc_final: 0.7736 (tpt-90) REVERT: k 65 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7393 (mmt) REVERT: k 77 HIS cc_start: 0.7331 (m-70) cc_final: 0.7118 (m-70) REVERT: k 125 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7420 (tptm) REVERT: l 60 SER cc_start: 0.7899 (t) cc_final: 0.7417 (t) REVERT: o 59 MET cc_start: 0.8055 (mtt) cc_final: 0.7763 (mtt) REVERT: p 50 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8571 (pt) REVERT: p 74 ILE cc_start: 0.9091 (pt) cc_final: 0.8797 (pt) REVERT: q 4 ARG cc_start: 0.6824 (tpm170) cc_final: 0.6485 (tpm170) REVERT: q 28 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7635 (mm-30) REVERT: r 27 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7455 (t70) REVERT: r 35 LYS cc_start: 0.8851 (mptt) cc_final: 0.8574 (mptt) REVERT: r 47 ARG cc_start: 0.8743 (mtp85) cc_final: 0.8509 (mtp85) outliers start: 78 outliers final: 59 residues processed: 360 average time/residue: 0.5264 time to fit residues: 298.6125 Evaluate side-chains 364 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 300 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 0.0170 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38419 Z= 0.305 Angle : 0.616 11.241 57451 Z= 0.314 Chirality : 0.037 0.233 7345 Planarity : 0.005 0.061 3085 Dihedral : 23.480 177.410 19057 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.30 % Rotamer: Outliers : 6.88 % Allowed : 22.55 % Favored : 70.56 % 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: -2.07 (0.22), residues: 1380 helix: -0.21 (0.23), residues: 487 sheet: -2.10 (0.32), residues: 230 loop : -1.97 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP k 44 HIS 0.009 0.002 HIS o 51 PHE 0.017 0.002 PHE k 61 TYR 0.023 0.002 TYR f 60 ARG 0.005 0.001 ARG d 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 300 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.7689 (ptmt) cc_final: 0.7167 (tptm) REVERT: b 151 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6508 (pp) REVERT: d 3 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8238 (tpt-90) REVERT: d 119 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8392 (pt) REVERT: d 120 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8348 (mt) REVERT: e 43 ASN cc_start: 0.7840 (p0) cc_final: 0.7584 (p0) REVERT: f 74 ASP cc_start: 0.8379 (p0) cc_final: 0.7682 (p0) REVERT: f 79 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8309 (mt) REVERT: h 10 MET cc_start: 0.7916 (ttt) cc_final: 0.7691 (ttt) REVERT: h 39 ILE cc_start: 0.9179 (mm) cc_final: 0.8897 (mt) REVERT: h 61 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7665 (ttm170) REVERT: h 98 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8489 (mp) REVERT: k 24 ARG cc_start: 0.7938 (tpt-90) cc_final: 0.7671 (tpt-90) REVERT: k 65 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7376 (mmt) REVERT: k 125 LYS cc_start: 0.8223 (tmmt) cc_final: 0.7455 (tptm) REVERT: l 60 SER cc_start: 0.7812 (t) cc_final: 0.7290 (t) REVERT: l 109 HIS cc_start: 0.7751 (p-80) cc_final: 0.7519 (p90) REVERT: o 59 MET cc_start: 0.7996 (mtt) cc_final: 0.7729 (mtt) REVERT: p 74 ILE cc_start: 0.9041 (pt) cc_final: 0.8803 (pt) REVERT: q 4 ARG cc_start: 0.6997 (tpm170) cc_final: 0.6645 (tpm170) REVERT: r 27 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7572 (t70) REVERT: r 35 LYS cc_start: 0.8972 (mptt) cc_final: 0.8735 (mptt) outliers start: 83 outliers final: 68 residues processed: 351 average time/residue: 0.5290 time to fit residues: 292.8607 Evaluate side-chains 371 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 295 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38419 Z= 0.269 Angle : 0.596 11.301 57451 Z= 0.304 Chirality : 0.036 0.230 7345 Planarity : 0.004 0.064 3085 Dihedral : 23.463 177.606 19057 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 6.88 % Allowed : 23.13 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.87 (0.22), residues: 1380 helix: -0.00 (0.23), residues: 479 sheet: -2.04 (0.33), residues: 233 loop : -1.85 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP k 44 HIS 0.015 0.002 HIS o 51 PHE 0.016 0.002 PHE k 61 TYR 0.027 0.002 TYR f 60 ARG 0.005 0.001 ARG d 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 300 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.7903 (t0) cc_final: 0.7559 (t0) REVERT: b 28 LYS cc_start: 0.7606 (ptmt) cc_final: 0.7100 (tptm) REVERT: b 151 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6506 (pp) REVERT: d 3 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8172 (tpt-90) REVERT: d 119 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8403 (pt) REVERT: d 120 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8351 (mt) REVERT: e 43 ASN cc_start: 0.7818 (p0) cc_final: 0.7587 (p0) REVERT: e 45 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7907 (mtp-110) REVERT: f 74 ASP cc_start: 0.8326 (p0) cc_final: 0.7462 (p0) REVERT: f 79 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8213 (mt) REVERT: h 10 MET cc_start: 0.7891 (ttt) cc_final: 0.7641 (ttt) REVERT: h 39 ILE cc_start: 0.9171 (mm) cc_final: 0.8886 (mt) REVERT: h 61 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7667 (ttm170) REVERT: h 98 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8466 (mp) REVERT: k 65 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7279 (mmt) REVERT: k 77 HIS cc_start: 0.7446 (m-70) cc_final: 0.7128 (m-70) REVERT: k 125 LYS cc_start: 0.8209 (tmmt) cc_final: 0.7448 (tptm) REVERT: l 60 SER cc_start: 0.7927 (t) cc_final: 0.7482 (t) REVERT: o 59 MET cc_start: 0.8133 (mtt) cc_final: 0.7848 (mtt) REVERT: p 74 ILE cc_start: 0.9068 (pt) cc_final: 0.8834 (pt) REVERT: q 4 ARG cc_start: 0.6929 (tpm170) cc_final: 0.6629 (tpm170) REVERT: r 27 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7557 (t70) REVERT: r 35 LYS cc_start: 0.8994 (mptt) cc_final: 0.8721 (mptt) REVERT: r 73 LEU cc_start: 0.9288 (mt) cc_final: 0.9031 (mt) outliers start: 83 outliers final: 70 residues processed: 353 average time/residue: 0.5390 time to fit residues: 299.2188 Evaluate side-chains 375 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 297 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 38419 Z= 0.514 Angle : 0.771 11.403 57451 Z= 0.388 Chirality : 0.045 0.305 7345 Planarity : 0.006 0.063 3085 Dihedral : 23.577 174.817 19057 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.00 % Favored : 89.93 % Rotamer: Outliers : 7.38 % Allowed : 23.05 % Favored : 69.57 % 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: -2.19 (0.22), residues: 1380 helix: -0.36 (0.23), residues: 490 sheet: -2.16 (0.31), residues: 247 loop : -1.98 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP h 132 HIS 0.016 0.002 HIS o 51 PHE 0.019 0.003 PHE l 28 TYR 0.034 0.003 TYR f 60 ARG 0.008 0.001 ARG q 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 303 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7302 (mmm) cc_final: 0.6650 (mmm) REVERT: b 28 LYS cc_start: 0.7662 (ptmt) cc_final: 0.7129 (tptm) REVERT: b 151 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6470 (pp) REVERT: d 3 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8235 (tpt-90) REVERT: d 119 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8466 (pt) REVERT: d 120 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8410 (mt) REVERT: e 41 ASP cc_start: 0.8515 (p0) cc_final: 0.8252 (p0) REVERT: e 43 ASN cc_start: 0.8034 (p0) cc_final: 0.7769 (p0) REVERT: f 70 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.6952 (p0) REVERT: f 74 ASP cc_start: 0.8490 (p0) cc_final: 0.7625 (p0) REVERT: f 79 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8232 (mt) REVERT: h 22 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.8133 (m-70) REVERT: h 39 ILE cc_start: 0.9204 (mm) cc_final: 0.8912 (mt) REVERT: h 61 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7710 (ttm170) REVERT: h 98 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8513 (mp) REVERT: k 65 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7339 (mmt) REVERT: k 77 HIS cc_start: 0.7622 (m-70) cc_final: 0.7293 (m-70) REVERT: k 125 LYS cc_start: 0.8244 (tmmt) cc_final: 0.7426 (tptm) REVERT: l 60 SER cc_start: 0.7823 (t) cc_final: 0.7302 (t) REVERT: l 75 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: p 74 ILE cc_start: 0.9173 (pt) cc_final: 0.8966 (pt) REVERT: q 4 ARG cc_start: 0.7140 (tpm170) cc_final: 0.6831 (tpm170) REVERT: r 27 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7355 (t70) REVERT: t 23 SER cc_start: 0.9008 (t) cc_final: 0.8712 (m) REVERT: t 72 ASP cc_start: 0.8660 (m-30) cc_final: 0.8383 (m-30) outliers start: 89 outliers final: 72 residues processed: 361 average time/residue: 0.5357 time to fit residues: 304.5937 Evaluate side-chains 374 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 291 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 70 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.0470 chunk 208 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 201 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 ASN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38419 Z= 0.147 Angle : 0.559 11.638 57451 Z= 0.286 Chirality : 0.033 0.246 7345 Planarity : 0.004 0.066 3085 Dihedral : 23.455 178.449 19056 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.14 % Allowed : 25.54 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1380 helix: 0.29 (0.24), residues: 478 sheet: -1.98 (0.33), residues: 232 loop : -1.74 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 43 HIS 0.008 0.001 HIS o 51 PHE 0.018 0.001 PHE d 79 TYR 0.022 0.002 TYR q 30 ARG 0.007 0.001 ARG d 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 313 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.7889 (t0) cc_final: 0.7551 (t0) REVERT: b 28 LYS cc_start: 0.7591 (ptmt) cc_final: 0.7095 (tptm) REVERT: d 119 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8377 (pt) REVERT: e 60 ILE cc_start: 0.8429 (pt) cc_final: 0.8177 (mt) REVERT: f 1 MET cc_start: 0.5617 (tpt) cc_final: 0.4677 (tpp) REVERT: f 70 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6506 (p0) REVERT: f 74 ASP cc_start: 0.8301 (p0) cc_final: 0.7393 (p0) REVERT: f 78 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.8307 (tmm-80) REVERT: f 79 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8071 (mt) REVERT: h 10 MET cc_start: 0.7698 (ttt) cc_final: 0.7406 (ttt) REVERT: h 22 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8025 (m-70) REVERT: h 39 ILE cc_start: 0.9151 (mm) cc_final: 0.8873 (mt) REVERT: h 98 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8499 (mp) REVERT: k 24 ARG cc_start: 0.7795 (tpt-90) cc_final: 0.7578 (tpt90) REVERT: k 65 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7272 (mmt) REVERT: k 125 LYS cc_start: 0.8157 (tmmt) cc_final: 0.7439 (tptm) REVERT: l 60 SER cc_start: 0.7801 (t) cc_final: 0.7373 (t) REVERT: o 74 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7070 (p0) REVERT: p 50 ILE cc_start: 0.8753 (pt) cc_final: 0.8549 (pt) REVERT: p 62 ASN cc_start: 0.8103 (m110) cc_final: 0.7713 (m110) REVERT: p 74 ILE cc_start: 0.9031 (pt) cc_final: 0.8779 (pt) REVERT: q 4 ARG cc_start: 0.6801 (tpm170) cc_final: 0.6507 (tpm170) REVERT: r 27 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7514 (t70) REVERT: r 35 LYS cc_start: 0.8760 (mptt) cc_final: 0.8461 (mptt) REVERT: t 72 ASP cc_start: 0.8695 (m-30) cc_final: 0.8456 (m-30) outliers start: 62 outliers final: 44 residues processed: 350 average time/residue: 0.5424 time to fit residues: 301.6499 Evaluate side-chains 346 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 294 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 157 MET Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 70 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 0.0980 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 GLN k 77 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38419 Z= 0.159 Angle : 0.539 11.108 57451 Z= 0.275 Chirality : 0.032 0.219 7345 Planarity : 0.004 0.075 3085 Dihedral : 23.328 179.648 19056 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.48 % Allowed : 26.62 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1380 helix: 0.53 (0.24), residues: 478 sheet: -1.79 (0.33), residues: 231 loop : -1.62 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP f 43 HIS 0.018 0.002 HIS o 50 PHE 0.020 0.002 PHE d 79 TYR 0.025 0.002 TYR f 60 ARG 0.007 0.001 ARG d 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 298 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.7933 (t0) cc_final: 0.7589 (t0) REVERT: b 28 LYS cc_start: 0.7599 (ptmt) cc_final: 0.7094 (tptm) REVERT: d 119 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8352 (pt) REVERT: f 1 MET cc_start: 0.5484 (tpt) cc_final: 0.4586 (tpp) REVERT: f 70 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.6505 (p0) REVERT: f 74 ASP cc_start: 0.8474 (p0) cc_final: 0.7628 (p0) REVERT: f 79 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8031 (mt) REVERT: h 10 MET cc_start: 0.7747 (ttt) cc_final: 0.7458 (ttt) REVERT: h 22 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.7991 (m-70) REVERT: h 39 ILE cc_start: 0.9154 (mm) cc_final: 0.8879 (mt) REVERT: h 98 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8476 (mp) REVERT: k 24 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.7540 (tpt90) REVERT: k 65 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7253 (mmt) REVERT: k 125 LYS cc_start: 0.8166 (tmmt) cc_final: 0.7494 (tptm) REVERT: l 60 SER cc_start: 0.7524 (t) cc_final: 0.7001 (t) REVERT: l 102 ASP cc_start: 0.8420 (t0) cc_final: 0.8210 (t0) REVERT: o 47 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8089 (ptpp) REVERT: p 62 ASN cc_start: 0.7977 (m110) cc_final: 0.7500 (m110) REVERT: p 74 ILE cc_start: 0.8982 (pt) cc_final: 0.8753 (pt) REVERT: q 4 ARG cc_start: 0.6651 (tpm170) cc_final: 0.6393 (tpm170) REVERT: r 27 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7474 (t70) outliers start: 54 outliers final: 42 residues processed: 329 average time/residue: 0.4783 time to fit residues: 247.0932 Evaluate side-chains 338 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 289 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 GLN Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 70 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: