Starting phenix.real_space_refine on Thu Mar 21 04:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/03_2024/8f2r_28825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/03_2024/8f2r_28825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/03_2024/8f2r_28825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/03_2024/8f2r_28825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/03_2024/8f2r_28825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/03_2024/8f2r_28825.pdb" } resolution = 3.12 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= -0.000 sd= 0.029 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 S 68 5.16 5 C 9189 2.51 5 N 2499 2.21 5 O 2748 1.98 5 H 14772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 66": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ASP 190": "OD1" <-> "OD2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J ASP 199": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29276 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2940 Classifications: {'peptide': 187} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3240 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain: "C" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3095 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "D" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3093 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "E" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3239 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1239 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3186 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "H" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2928 Classifications: {'peptide': 179} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "I" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3104 Classifications: {'peptide': 198} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "J" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3212 Classifications: {'peptide': 198} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Time building chain proxies: 12.45, per 1000 atoms: 0.43 Number of scatterers: 29276 At special positions: 0 Unit cell: (121.408, 132.248, 132.248, 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 68 16.00 O 2748 8.00 N 2499 7.00 C 9189 6.00 H 14772 1.00 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: 23.14 Conformation dependent library (CDL) restraints added in 3.4 seconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3524 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 5 sheets defined 64.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.805A pdb=" N LEU A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 31 through 40 Processing helix chain 'A' and resid 44 through 64 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 87 through 113 removed outlier: 7.412A pdb=" N THR A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 20 through 38 removed outlier: 4.400A pdb=" N ARG B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.997A pdb=" N TYR B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 76 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 168 through 188 removed outlier: 3.933A pdb=" N MET B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 55 through 76 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 93 through 117 removed outlier: 5.040A pdb=" N ASN C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 4.209A pdb=" N LEU C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 12 through 24 removed outlier: 4.230A pdb=" N SER D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 42 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 61 through 83 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.606A pdb=" N CYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Proline residue: D 116 - end of helix Processing helix chain 'D' and resid 178 through 199 removed outlier: 3.635A pdb=" N SER D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 78 through 99 removed outlier: 3.726A pdb=" N LEU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 119 through 132 Processing helix chain 'E' and resid 133 through 143 removed outlier: 4.065A pdb=" N LEU E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 removed outlier: 4.257A pdb=" N ALA E 147 " --> pdb=" O GLN E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 193 through 222 removed outlier: 3.638A pdb=" N ARG E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 4.105A pdb=" N VAL F 15 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 85 Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.732A pdb=" N GLY G 16 " --> pdb=" O PRO G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 Processing helix chain 'G' and resid 46 through 62 Processing helix chain 'G' and resid 64 through 86 removed outlier: 4.831A pdb=" N VAL G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 88 through 100 Processing helix chain 'G' and resid 102 through 115 Processing helix chain 'G' and resid 116 through 126 Processing helix chain 'G' and resid 179 through 198 Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.581A pdb=" N ARG H 11 " --> pdb=" O PRO H 8 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 14 " --> pdb=" O ARG H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 18 No H-bonds generated for 'chain 'H' and resid 16 through 18' Processing helix chain 'H' and resid 19 through 32 removed outlier: 3.516A pdb=" N LEU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 42 Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.918A pdb=" N ALA H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 78 Processing helix chain 'H' and resid 83 through 96 Processing helix chain 'H' and resid 97 through 111 removed outlier: 3.749A pdb=" N ILE H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 183 removed outlier: 3.702A pdb=" N VAL H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 14 through 18 Processing helix chain 'I' and resid 20 through 34 removed outlier: 3.706A pdb=" N VAL I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 4.157A pdb=" N LYS I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 75 Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'I' and resid 91 through 117 removed outlier: 4.004A pdb=" N LEU I 97 " --> pdb=" O ASN I 93 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 161 Processing helix chain 'I' and resid 174 through 198 removed outlier: 4.622A pdb=" N ARG I 187 " --> pdb=" O ASP I 183 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE I 188 " --> pdb=" O GLY I 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.514A pdb=" N LEU J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 62 Processing helix chain 'J' and resid 64 through 85 Processing helix chain 'J' and resid 88 through 100 Processing helix chain 'J' and resid 102 through 126 removed outlier: 5.911A pdb=" N GLN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 201 Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.576A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TRP A 124 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER I 136 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 126 " --> pdb=" O THR I 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 130 " --> pdb=" O VAL I 130 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL I 130 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER A 132 " --> pdb=" O TRP I 128 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP I 128 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU I 123 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN I 154 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP I 125 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL I 144 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 167 removed outlier: 5.704A pdb=" N ASN B 155 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR B 124 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TRP B 129 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER H 130 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 131 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 124 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER B 137 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP H 122 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP H 146 " --> pdb=" O GLN H 118 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE H 120 " --> pdb=" O HIS H 144 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS H 144 " --> pdb=" O PHE H 120 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP H 122 " --> pdb=" O SER H 142 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER H 142 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL H 124 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU H 140 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU H 126 " --> pdb=" O MET H 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET H 138 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 165 through 170 removed outlier: 6.143A pdb=" N GLN C 156 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE C 125 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP C 130 " --> pdb=" O HIS J 147 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS J 147 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 132 " --> pdb=" O MET J 145 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU J 141 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR C 138 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP J 139 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY J 163 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL J 137 " --> pdb=" O GLN J 161 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN J 161 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP J 139 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL J 159 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU J 141 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN J 157 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA J 158 " --> pdb=" O PHE J 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 170 through 177 removed outlier: 3.650A pdb=" N GLY D 133 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 162 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU D 131 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP D 136 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER F 32 " --> pdb=" O TRP D 136 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 138 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU F 26 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER D 144 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TRP F 24 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU F 19 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA F 50 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 187 through 192 removed outlier: 6.741A pdb=" N SER E 175 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL E 159 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 177 " --> pdb=" O TRP E 157 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 157 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN E 179 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE E 155 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 181 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP E 157 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER G 147 " --> pdb=" O TRP E 157 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL E 159 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU G 134 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS G 165 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP G 136 " --> pdb=" O VAL G 163 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.29 Time building geometry restraints manager: 23.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14745 1.03 - 1.22: 28 1.22 - 1.42: 5937 1.42 - 1.62: 8696 1.62 - 1.81: 109 Bond restraints: 29515 Sorted by residual: bond pdb=" CB PRO H 71 " pdb=" CG PRO H 71 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 bond pdb=" CG GLN I 114 " pdb=" CD GLN I 114 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" N LEU E 149 " pdb=" CA LEU E 149 " ideal model delta sigma weight residual 1.454 1.474 -0.021 1.74e-02 3.30e+03 1.44e+00 bond pdb=" CG PRO H 71 " pdb=" CD PRO H 71 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.33e+00 bond pdb=" CB ASP F 51 " pdb=" CG ASP F 51 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.33e+00 ... (remaining 29510 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.46: 273 105.46 - 112.63: 35078 112.63 - 119.80: 7892 119.80 - 126.96: 10157 126.96 - 134.13: 163 Bond angle restraints: 53563 Sorted by residual: angle pdb=" CA PRO H 71 " pdb=" N PRO H 71 " pdb=" CD PRO H 71 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 angle pdb=" N PRO H 71 " pdb=" CD PRO H 71 " pdb=" CG PRO H 71 " ideal model delta sigma weight residual 103.20 98.30 4.90 1.50e+00 4.44e-01 1.07e+01 angle pdb=" N ASN C 109 " pdb=" CA ASN C 109 " pdb=" C ASN C 109 " ideal model delta sigma weight residual 111.82 115.57 -3.75 1.16e+00 7.43e-01 1.05e+01 angle pdb=" CA TYR F 40 " pdb=" CB TYR F 40 " pdb=" CG TYR F 40 " ideal model delta sigma weight residual 113.90 119.56 -5.66 1.80e+00 3.09e-01 9.87e+00 angle pdb=" N MET D 128 " pdb=" CA MET D 128 " pdb=" C MET D 128 " ideal model delta sigma weight residual 109.39 114.18 -4.79 1.59e+00 3.96e-01 9.08e+00 ... (remaining 53558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12404 17.81 - 35.62: 838 35.62 - 53.42: 257 53.42 - 71.23: 205 71.23 - 89.04: 24 Dihedral angle restraints: 13728 sinusoidal: 7618 harmonic: 6110 Sorted by residual: dihedral pdb=" CA CYS C 170 " pdb=" C CYS C 170 " pdb=" N SER C 171 " pdb=" CA SER C 171 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASP E 63 " pdb=" C ASP E 63 " pdb=" N CYS E 64 " pdb=" CA CYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ILE A 138 " pdb=" C ILE A 138 " pdb=" N HIS A 139 " pdb=" CA HIS A 139 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 13725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1714 0.043 - 0.087: 455 0.087 - 0.130: 112 0.130 - 0.174: 25 0.174 - 0.217: 3 Chirality restraints: 2309 Sorted by residual: chirality pdb=" CA ARG B 141 " pdb=" N ARG B 141 " pdb=" C ARG B 141 " pdb=" CB ARG B 141 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR C 145 " pdb=" N TYR C 145 " pdb=" C TYR C 145 " pdb=" CB TYR C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2306 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 170 " -0.203 9.50e-02 1.11e+02 7.87e-02 4.08e+01 pdb=" NE ARG E 170 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG E 170 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG E 170 " 0.084 2.00e-02 2.50e+03 pdb=" NH2 ARG E 170 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG E 170 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG E 170 " -0.079 2.00e-02 2.50e+03 pdb="HH21 ARG E 170 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 170 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 110 " -0.122 9.50e-02 1.11e+02 5.79e-02 3.98e+01 pdb=" NE ARG I 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG I 110 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 110 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG I 110 " 0.071 2.00e-02 2.50e+03 pdb="HH11 ARG I 110 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG I 110 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG I 110 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG I 110 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " 0.144 9.50e-02 1.11e+02 6.17e-02 3.65e+01 pdb=" NE ARG A 125 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.075 2.00e-02 2.50e+03 pdb="HH11 ARG A 125 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 125 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 125 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 125 " 0.076 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 750 2.12 - 2.74: 53464 2.74 - 3.36: 83524 3.36 - 3.98: 102357 3.98 - 4.60: 163404 Nonbonded interactions: 403499 Sorted by model distance: nonbonded pdb=" HH TYR D 140 " pdb=" OE1 GLU D 151 " model vdw 1.504 1.850 nonbonded pdb=" OE1 GLU A 162 " pdb=" HG1 THR F 16 " model vdw 1.510 1.850 nonbonded pdb=" OE1 GLU H 49 " pdb=" H GLU H 49 " model vdw 1.515 1.850 nonbonded pdb=" OE1 GLN E 120 " pdb=" H GLN E 120 " model vdw 1.520 1.850 nonbonded pdb=" OE1 GLN F 18 " pdb=" H GLN F 18 " model vdw 1.565 1.850 ... (remaining 403494 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.430 Extract box with map and model: 11.310 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 87.340 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.004 0.068 14743 Z= 0.259 Angle : 0.797 6.379 19911 Z= 0.482 Chirality : 0.043 0.217 2309 Planarity : 0.010 0.123 2547 Dihedral : 15.266 89.040 5566 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.20 % Favored : 97.63 % Rotamer: Outliers : 0.12 % Allowed : 11.27 % Favored : 88.61 % 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: 0.09 (0.18), residues: 1817 helix: 0.07 (0.14), residues: 1093 sheet: 0.77 (0.28), residues: 287 loop : -0.03 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP E 148 HIS 0.009 0.002 HIS J 181 PHE 0.021 0.003 PHE G 96 TYR 0.031 0.005 TYR C 134 ARG 0.024 0.003 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 128 MET cc_start: 0.6232 (mmm) cc_final: 0.5845 (mmm) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.7473 time to fit residues: 196.5262 Evaluate side-chains 157 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14743 Z= 0.216 Angle : 0.572 5.286 19911 Z= 0.309 Chirality : 0.038 0.186 2309 Planarity : 0.005 0.068 2547 Dihedral : 4.722 21.838 1945 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.38 % Favored : 98.51 % Rotamer: Outliers : 1.18 % Allowed : 10.59 % Favored : 88.24 % 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: 1.54 (0.19), residues: 1817 helix: 1.49 (0.15), residues: 1099 sheet: 0.51 (0.28), residues: 297 loop : 0.43 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 122 HIS 0.006 0.001 HIS J 147 PHE 0.015 0.002 PHE C 11 TYR 0.020 0.002 TYR F 40 ARG 0.005 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7239 (mtp) cc_final: 0.6975 (mtp) REVERT: E 65 ARG cc_start: 0.5130 (mtm-85) cc_final: 0.4167 (mmt180) REVERT: G 148 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8099 (t) REVERT: H 53 HIS cc_start: 0.6244 (m-70) cc_final: 0.6014 (m-70) REVERT: I 92 GLN cc_start: 0.5086 (mp10) cc_final: 0.4439 (mm-40) outliers start: 19 outliers final: 15 residues processed: 179 average time/residue: 0.7588 time to fit residues: 192.3340 Evaluate side-chains 167 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14743 Z= 0.219 Angle : 0.522 5.338 19911 Z= 0.279 Chirality : 0.037 0.167 2309 Planarity : 0.004 0.052 2547 Dihedral : 4.322 24.392 1945 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.73 % Allowed : 10.90 % Favored : 87.37 % 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: 1.84 (0.20), residues: 1817 helix: 1.83 (0.15), residues: 1104 sheet: 0.51 (0.28), residues: 291 loop : 0.28 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 46 HIS 0.006 0.001 HIS I 91 PHE 0.015 0.001 PHE G 141 TYR 0.020 0.001 TYR F 40 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.5939 (mtm-85) cc_final: 0.4196 (mmt-90) REVERT: H 34 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7364 (mtm180) outliers start: 28 outliers final: 20 residues processed: 180 average time/residue: 0.6889 time to fit residues: 172.7856 Evaluate side-chains 172 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14743 Z= 0.174 Angle : 0.489 5.877 19911 Z= 0.259 Chirality : 0.035 0.165 2309 Planarity : 0.004 0.046 2547 Dihedral : 4.111 28.830 1945 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.46 % Rotamer: Outliers : 1.55 % Allowed : 11.39 % Favored : 87.06 % 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 (0.20), residues: 1817 helix: 2.10 (0.16), residues: 1104 sheet: 0.52 (0.28), residues: 283 loop : 0.17 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 PHE 0.014 0.001 PHE G 141 TYR 0.016 0.001 TYR F 40 ARG 0.003 0.000 ARG J 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 128 MET cc_start: 0.6588 (mmt) cc_final: 0.6325 (mmt) REVERT: E 65 ARG cc_start: 0.5958 (mtm-85) cc_final: 0.4161 (mmt180) REVERT: G 148 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8626 (p) REVERT: H 34 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7331 (mtm-85) REVERT: H 56 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7045 (mt-10) outliers start: 25 outliers final: 18 residues processed: 176 average time/residue: 0.7165 time to fit residues: 174.6127 Evaluate side-chains 170 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 chunk 2 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14743 Z= 0.205 Angle : 0.491 4.873 19911 Z= 0.261 Chirality : 0.036 0.149 2309 Planarity : 0.004 0.046 2547 Dihedral : 4.009 24.388 1945 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.80 % Allowed : 11.33 % Favored : 86.87 % 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: 2.07 (0.20), residues: 1817 helix: 2.16 (0.16), residues: 1109 sheet: 0.37 (0.27), residues: 291 loop : 0.04 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 PHE 0.014 0.001 PHE G 141 TYR 0.019 0.001 TYR F 40 ARG 0.005 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6752 (tp) REVERT: E 65 ARG cc_start: 0.6051 (mtm-85) cc_final: 0.4249 (mmp-170) REVERT: G 148 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8666 (p) REVERT: H 34 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7523 (mtm-85) outliers start: 29 outliers final: 22 residues processed: 175 average time/residue: 0.6776 time to fit residues: 166.4687 Evaluate side-chains 176 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN H 53 HIS H 86 HIS ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14743 Z= 0.169 Angle : 0.477 5.377 19911 Z= 0.251 Chirality : 0.035 0.145 2309 Planarity : 0.004 0.045 2547 Dihedral : 3.864 23.425 1945 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.54 % Favored : 98.40 % Rotamer: Outliers : 1.73 % Allowed : 11.95 % Favored : 86.32 % 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: 2.25 (0.20), residues: 1817 helix: 2.37 (0.16), residues: 1103 sheet: 0.37 (0.28), residues: 292 loop : 0.02 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 PHE 0.014 0.001 PHE G 141 TYR 0.015 0.001 TYR F 40 ARG 0.005 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 MET cc_start: 0.8519 (tpt) cc_final: 0.8137 (tpt) REVERT: C 99 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6795 (tp) REVERT: D 128 MET cc_start: 0.6554 (mmt) cc_final: 0.6322 (mtp) REVERT: E 65 ARG cc_start: 0.6090 (mtm-85) cc_final: 0.4325 (mmp-170) REVERT: G 137 MET cc_start: 0.7376 (ttt) cc_final: 0.7091 (ttt) REVERT: G 148 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8688 (p) REVERT: H 34 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7324 (mtm-85) outliers start: 28 outliers final: 21 residues processed: 183 average time/residue: 0.7702 time to fit residues: 197.4979 Evaluate side-chains 176 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 96 optimal weight: 0.0270 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 106 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14743 Z= 0.224 Angle : 0.501 5.710 19911 Z= 0.265 Chirality : 0.036 0.143 2309 Planarity : 0.004 0.044 2547 Dihedral : 3.885 25.181 1945 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.98 % Allowed : 11.89 % Favored : 86.13 % 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: 2.14 (0.20), residues: 1817 helix: 2.33 (0.16), residues: 1104 sheet: 0.35 (0.27), residues: 291 loop : -0.22 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 46 HIS 0.010 0.001 HIS H 53 PHE 0.013 0.001 PHE F 71 TYR 0.017 0.001 TYR F 40 ARG 0.004 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7102 (tp) REVERT: D 1 MET cc_start: 0.6775 (mmt) cc_final: 0.6367 (mmt) REVERT: E 65 ARG cc_start: 0.6207 (mtm-85) cc_final: 0.4435 (mmp-170) REVERT: G 137 MET cc_start: 0.7426 (ttt) cc_final: 0.7133 (ttt) REVERT: H 34 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7634 (mtm-85) outliers start: 32 outliers final: 26 residues processed: 181 average time/residue: 0.7044 time to fit residues: 176.6796 Evaluate side-chains 178 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 86 HIS Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** H 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14743 Z= 0.249 Angle : 0.520 5.815 19911 Z= 0.276 Chirality : 0.036 0.147 2309 Planarity : 0.004 0.050 2547 Dihedral : 3.924 26.371 1945 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 11.76 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.20), residues: 1817 helix: 2.30 (0.16), residues: 1104 sheet: 0.27 (0.27), residues: 293 loop : -0.42 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 46 HIS 0.007 0.001 HIS B 153 PHE 0.015 0.001 PHE F 71 TYR 0.017 0.001 TYR F 40 ARG 0.010 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7235 (tp) REVERT: E 65 ARG cc_start: 0.6284 (mtm-85) cc_final: 0.4413 (mmt-90) REVERT: G 137 MET cc_start: 0.7473 (ttt) cc_final: 0.7139 (ttt) REVERT: H 34 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7505 (mtm-85) outliers start: 35 outliers final: 27 residues processed: 177 average time/residue: 0.6991 time to fit residues: 172.2732 Evaluate side-chains 173 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 0.0170 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14743 Z= 0.170 Angle : 0.481 5.968 19911 Z= 0.253 Chirality : 0.035 0.200 2309 Planarity : 0.004 0.044 2547 Dihedral : 3.770 24.099 1945 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.60 % Favored : 98.35 % Rotamer: Outliers : 1.67 % Allowed : 12.45 % Favored : 85.88 % 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: 2.26 (0.20), residues: 1817 helix: 2.50 (0.16), residues: 1104 sheet: 0.34 (0.27), residues: 293 loop : -0.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 46 HIS 0.006 0.001 HIS J 147 PHE 0.013 0.001 PHE F 71 TYR 0.013 0.001 TYR F 40 ARG 0.005 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7283 (tp) REVERT: E 65 ARG cc_start: 0.6277 (mtm-85) cc_final: 0.4383 (mmt-90) REVERT: H 34 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7238 (mtm180) outliers start: 27 outliers final: 25 residues processed: 175 average time/residue: 0.6959 time to fit residues: 168.9136 Evaluate side-chains 178 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 86 HIS Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14743 Z= 0.270 Angle : 0.534 6.595 19911 Z= 0.284 Chirality : 0.037 0.151 2309 Planarity : 0.004 0.046 2547 Dihedral : 3.903 25.867 1945 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 12.63 % Favored : 85.82 % 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: 2.00 (0.20), residues: 1817 helix: 2.33 (0.16), residues: 1104 sheet: 0.15 (0.27), residues: 294 loop : -0.52 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 46 HIS 0.009 0.001 HIS B 153 PHE 0.014 0.001 PHE F 71 TYR 0.018 0.001 TYR F 40 ARG 0.007 0.001 ARG E 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7435 (tp) REVERT: E 65 ARG cc_start: 0.6377 (mtm-85) cc_final: 0.4532 (mmp-170) REVERT: H 34 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7393 (mtm180) REVERT: H 86 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6704 (m170) outliers start: 25 outliers final: 21 residues processed: 166 average time/residue: 0.6751 time to fit residues: 159.1851 Evaluate side-chains 168 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 86 HIS Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.209523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140856 restraints weight = 52915.182| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.62 r_work: 0.3560 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14743 Z= 0.175 Angle : 0.489 6.030 19911 Z= 0.257 Chirality : 0.035 0.144 2309 Planarity : 0.004 0.046 2547 Dihedral : 3.765 24.314 1945 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.55 % Allowed : 12.57 % Favored : 85.88 % 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 (0.20), residues: 1817 helix: 2.52 (0.16), residues: 1104 sheet: 0.20 (0.27), residues: 295 loop : -0.42 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 46 HIS 0.006 0.001 HIS J 147 PHE 0.014 0.001 PHE F 71 TYR 0.013 0.001 TYR F 40 ARG 0.006 0.000 ARG E 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.55 seconds wall clock time: 115 minutes 41.73 seconds (6941.73 seconds total)