Starting phenix.real_space_refine on Sat Dec 16 13:19:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/12_2023/7bgd_12178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/12_2023/7bgd_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_12178/12_2023/7bgd_12178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/12_2023/7bgd_12178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/12_2023/7bgd_12178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgd_12178/12_2023/7bgd_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 18.44, per 1000 atoms: 0.52 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: 18.67 Conformation dependent library (CDL) restraints added in 2.5 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: 15.54 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: 29.30 Time building geometry restraints manager: 19.68 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: 20969 35.22 - 70.43: 2271 70.43 - 105.65: 307 105.65 - 140.86: 6 140.86 - 176.08: 12 Dihedral angle restraints: 23565 sinusoidal: 19511 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 23562 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 5.870 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 115.650 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.530 ------------------------------------------------------------------------------- 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 : 22.568 176.081 20949 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 : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 424 average time/residue: 0.5676 time to fit residues: 370.5410 Evaluate side-chains 332 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 324 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3649 time to fit residues: 7.9104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 100 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN b 190 ASN d 82 HIS ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN d 118 HIS ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN h 22 HIS k 18 ASN k 64 GLN k 77 HIS l 5 ASN l 6 GLN l 25 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 50 HIS p 46 ASN p 87 GLN t 42 ASN t 64 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 38419 Z= 0.365 Angle : 0.679 12.402 57451 Z= 0.349 Chirality : 0.040 0.325 7345 Planarity : 0.006 0.075 3085 Dihedral : 22.762 176.941 18079 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.39 % Allowed : 18.66 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.05 (0.19), residues: 481 sheet: -2.66 (0.30), residues: 237 loop : -2.47 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP k 44 HIS 0.013 0.002 HIS k 118 PHE 0.032 0.002 PHE k 61 TYR 0.020 0.002 TYR p 40 ARG 0.014 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 398 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 333 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 43 residues processed: 368 average time/residue: 0.5359 time to fit residues: 308.0648 Evaluate side-chains 363 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 320 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3359 time to fit residues: 29.0727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38419 Z= 0.162 Angle : 0.545 11.417 57451 Z= 0.282 Chirality : 0.033 0.216 7345 Planarity : 0.004 0.066 3085 Dihedral : 22.602 178.776 18079 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.48 % Allowed : 20.07 % Favored : 76.45 % 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: -2.64 (0.21), residues: 1380 helix: -0.83 (0.22), residues: 489 sheet: -2.37 (0.31), residues: 237 loop : -2.18 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP k 44 HIS 0.009 0.001 HIS o 51 PHE 0.012 0.001 PHE l 28 TYR 0.025 0.002 TYR q 30 ARG 0.024 0.001 ARG q 39 *********************** 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 387 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 345 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 372 average time/residue: 0.5225 time to fit residues: 305.1277 Evaluate side-chains 336 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 315 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3633 time to fit residues: 15.8678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 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: 5.9990 chunk 226 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 38419 Z= 0.466 Angle : 0.732 12.627 57451 Z= 0.371 Chirality : 0.043 0.278 7345 Planarity : 0.006 0.067 3085 Dihedral : 22.665 175.045 18079 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.64 % Allowed : 21.14 % Favored : 74.21 % 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: -0.69 (0.22), residues: 486 sheet: -2.27 (0.31), residues: 255 loop : -2.22 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP h 132 HIS 0.010 0.002 HIS o 51 PHE 0.020 0.002 PHE l 28 TYR 0.023 0.003 TYR p 40 ARG 0.011 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 372 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 316 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 41 residues processed: 351 average time/residue: 0.5284 time to fit residues: 290.6001 Evaluate side-chains 350 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 309 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3259 time to fit residues: 27.5385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38419 Z= 0.219 Angle : 0.587 11.839 57451 Z= 0.302 Chirality : 0.035 0.231 7345 Planarity : 0.004 0.075 3085 Dihedral : 22.626 177.345 18079 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.07 % Allowed : 23.22 % Favored : 74.71 % 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: -2.23 (0.22), residues: 1380 helix: -0.37 (0.23), residues: 490 sheet: -2.22 (0.33), residues: 231 loop : -2.02 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP k 44 HIS 0.010 0.002 HIS o 51 PHE 0.018 0.002 PHE l 28 TYR 0.018 0.002 TYR d 47 ARG 0.010 0.001 ARG o 64 *********************** 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 349 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 324 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 340 average time/residue: 0.5383 time to fit residues: 284.7098 Evaluate side-chains 329 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 313 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3660 time to fit residues: 12.9258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 47 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 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: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** 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** p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 38419 Z= 0.466 Angle : 0.729 11.231 57451 Z= 0.368 Chirality : 0.043 0.283 7345 Planarity : 0.006 0.071 3085 Dihedral : 22.656 175.462 18079 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.64 % Favored : 90.29 % Rotamer: Outliers : 3.23 % Allowed : 24.79 % Favored : 71.97 % 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: -2.34 (0.21), residues: 1380 helix: -0.40 (0.23), residues: 486 sheet: -2.20 (0.31), residues: 254 loop : -2.16 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP d 9 HIS 0.011 0.002 HIS o 51 PHE 0.021 0.002 PHE l 28 TYR 0.022 0.003 TYR p 40 ARG 0.010 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 350 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 311 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 336 average time/residue: 0.5664 time to fit residues: 300.3342 Evaluate side-chains 328 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 303 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3331 time to fit residues: 17.7568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 GLN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 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: 0.8107 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 38419 Z= 0.144 Angle : 0.550 11.360 57451 Z= 0.282 Chirality : 0.033 0.238 7345 Planarity : 0.004 0.066 3085 Dihedral : 22.540 179.349 18079 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.74 % Allowed : 25.29 % Favored : 72.97 % 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: -1.70 (0.22), residues: 1380 helix: 0.18 (0.24), residues: 478 sheet: -2.06 (0.33), residues: 230 loop : -1.73 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP p 60 HIS 0.011 0.001 HIS o 51 PHE 0.019 0.001 PHE d 79 TYR 0.025 0.002 TYR d 197 ARG 0.006 0.001 ARG f 2 *********************** 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 333 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 312 time to evaluate : 2.058 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 322 average time/residue: 0.5426 time to fit residues: 272.7021 Evaluate side-chains 316 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 303 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3990 time to fit residues: 11.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 217 optimal weight: 0.6980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 ASN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 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: 0.8165 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 38419 Z= 0.254 Angle : 0.586 12.296 57451 Z= 0.299 Chirality : 0.035 0.227 7345 Planarity : 0.004 0.057 3085 Dihedral : 22.485 178.103 18079 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.66 % Allowed : 27.20 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1380 helix: 0.20 (0.24), residues: 478 sheet: -2.05 (0.33), residues: 233 loop : -1.71 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP k 44 HIS 0.011 0.002 HIS o 51 PHE 0.014 0.002 PHE l 28 TYR 0.038 0.002 TYR l 65 ARG 0.007 0.001 ARG f 46 *********************** 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 317 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 305 average time/residue: 0.5839 time to fit residues: 278.6293 Evaluate side-chains 313 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 298 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3471 time to fit residues: 12.1705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 201 optimal weight: 0.3980 chunk 210 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 GLN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** o 18 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: 0.8169 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 38419 Z= 0.264 Angle : 0.595 12.378 57451 Z= 0.303 Chirality : 0.035 0.229 7345 Planarity : 0.005 0.065 3085 Dihedral : 22.489 177.526 18079 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.41 % Favored : 91.52 % Rotamer: Outliers : 1.00 % Allowed : 27.11 % Favored : 71.89 % 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: -1.70 (0.22), residues: 1380 helix: 0.16 (0.23), residues: 484 sheet: -2.06 (0.32), residues: 238 loop : -1.71 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP k 44 HIS 0.011 0.002 HIS o 51 PHE 0.019 0.002 PHE d 79 TYR 0.026 0.002 TYR f 89 ARG 0.011 0.001 ARG h 61 *********************** 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 312 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 300 time to evaluate : 2.076 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 303 average time/residue: 0.5446 time to fit residues: 254.4847 Evaluate side-chains 307 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 296 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3134 time to fit residues: 8.6559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 0.0670 chunk 247 optimal weight: 0.3980 chunk 227 optimal weight: 0.0020 chunk 196 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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: