Starting phenix.real_space_refine on Fri Mar 15 22:40:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/03_2024/8do6_27593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/03_2024/8do6_27593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/03_2024/8do6_27593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/03_2024/8do6_27593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/03_2024/8do6_27593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/03_2024/8do6_27593.pdb" } resolution = 3.1 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= 0.039 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 61 5.49 5 S 24 5.16 5 C 8030 2.51 5 N 2198 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 77": "OE1" <-> "OE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12980 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 15, 'rna3p': 19} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 13} Link IDs: {'rna2p': 3, 'rna3p': 22} Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 926 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 951 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "H" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2671 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 1 Time building chain proxies: 7.50, per 1000 atoms: 0.58 Number of scatterers: 12980 At special positions: 0 Unit cell: (93.906, 95.598, 164.97, 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 24 16.00 P 61 15.00 O 2667 8.00 N 2198 7.00 C 8030 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: 5.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 20 sheets defined 40.8% alpha, 21.7% beta 17 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'E' and resid 47 through 65 Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.788A pdb=" N LEU E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.530A pdb=" N ASN E 114 " --> pdb=" O HIS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 178 removed outlier: 4.953A pdb=" N GLU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 64 Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.796A pdb=" N LEU G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 158 through 160 No H-bonds generated for 'chain 'G' and resid 158 through 160' Processing helix chain 'G' and resid 161 through 178 removed outlier: 4.080A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 188 Processing helix chain 'F' and resid 47 through 64 Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 104 through 114 removed outlier: 3.702A pdb=" N GLU F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 179 Processing helix chain 'F' and resid 184 through 188 removed outlier: 3.517A pdb=" N GLY F 188 " --> pdb=" O GLY F 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.625A pdb=" N ASN C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 removed outlier: 4.246A pdb=" N GLN C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 4.067A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.664A pdb=" N ASP C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.649A pdb=" N ILE C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.653A pdb=" N VAL D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 4.539A pdb=" N GLN D 54 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.581A pdb=" N ILE D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 136 removed outlier: 3.793A pdb=" N VAL D 131 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.708A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.727A pdb=" N THR B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 186 removed outlier: 4.480A pdb=" N TYR B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.870A pdb=" N LEU B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 53 removed outlier: 3.665A pdb=" N LYS H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.698A pdb=" N ASN H 61 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 83 removed outlier: 4.017A pdb=" N TYR H 78 " --> pdb=" O GLY H 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 91 removed outlier: 3.777A pdb=" N GLU H 88 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA H 91 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 147 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 211 through 230 Processing helix chain 'H' and resid 231 through 236 removed outlier: 4.013A pdb=" N GLU H 236 " --> pdb=" O GLY H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 246 Processing helix chain 'H' and resid 266 through 270 Processing helix chain 'H' and resid 271 through 276 removed outlier: 3.877A pdb=" N LYS H 276 " --> pdb=" O HIS H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 293 Processing helix chain 'H' and resid 296 through 300 Processing sheet with id=AA1, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.748A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL E 203 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS E 6 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR E 201 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER E 8 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 199 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR E 10 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR E 197 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU E 12 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS E 195 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.748A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLY B 194 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE E 98 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 119 through 125 Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'G' and resid 45 through 46 removed outlier: 4.198A pdb=" N SER G 3 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS G 4 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR G 10 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP G 196 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU G 12 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE G 194 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 122 through 123 Processing sheet with id=AA7, first strand: chain 'F' and resid 96 through 97 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.543A pdb=" N LYS F 4 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR F 201 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS F 6 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE F 199 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER F 8 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR F 197 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'F' and resid 123 through 124 Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.520A pdb=" N LYS D 26 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 59 removed outlier: 7.346A pdb=" N ALA B 159 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 12 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'B' and resid 124 through 133 Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 246 Processing sheet with id=AB8, first strand: chain 'B' and resid 281 through 284 Processing sheet with id=AB9, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.741A pdb=" N TYR H 6 " --> pdb=" O LEU H 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 205 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS H 4 " --> pdb=" O ILE H 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN H 5 " --> pdb=" O LEU H 335 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 19 through 24 removed outlier: 4.857A pdb=" N GLN H 22 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET H 119 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ILE H 193 " --> pdb=" O MET H 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 186 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP H 178 " --> pdb=" O MET H 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU H 188 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 13.748A pdb=" N LEU H 171 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N SER H 96 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE H 173 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS H 98 " --> pdb=" O ILE H 173 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLN H 175 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASN H 100 " --> pdb=" O GLN H 175 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE H 177 " --> pdb=" O ASN H 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 19 through 24 removed outlier: 4.857A pdb=" N GLN H 22 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET H 119 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ILE H 193 " --> pdb=" O MET H 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 186 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP H 178 " --> pdb=" O MET H 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU H 188 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN H 175 " --> pdb=" O THR H 315 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR H 315 " --> pdb=" O GLN H 175 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 1 1.21 - 1.36: 4132 1.36 - 1.51: 4418 1.51 - 1.66: 4745 1.66 - 1.81: 44 Bond restraints: 13340 Sorted by residual: bond pdb=" CG PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 1.503 1.065 0.438 3.40e-02 8.65e+02 1.66e+02 bond pdb=" N PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" CB PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CB ASN H 147 " pdb=" CG ASN H 147 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.39e+00 bond pdb=" CB GLU B 158 " pdb=" CG GLU B 158 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 13335 not shown) Histogram of bond angle deviations from ideal: 78.69 - 89.75: 2 89.75 - 100.81: 13 100.81 - 111.87: 6678 111.87 - 122.93: 10367 122.93 - 133.99: 1174 Bond angle restraints: 18234 Sorted by residual: angle pdb=" N PRO H 70 " pdb=" CD PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 103.20 78.69 24.51 1.50e+00 4.44e-01 2.67e+02 angle pdb=" CA PRO H 70 " pdb=" CB PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 104.50 89.09 15.41 1.90e+00 2.77e-01 6.58e+01 angle pdb=" CA PRO H 70 " pdb=" N PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 112.00 102.87 9.13 1.40e+00 5.10e-01 4.25e+01 angle pdb=" N PRO H 70 " pdb=" CA PRO H 70 " pdb=" CB PRO H 70 " ideal model delta sigma weight residual 102.60 97.16 5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" O4' A I 27 " pdb=" C1' A I 27 " pdb=" N9 A I 27 " ideal model delta sigma weight residual 108.20 114.47 -6.27 1.50e+00 4.44e-01 1.75e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 7718 34.52 - 69.04: 319 69.04 - 103.57: 38 103.57 - 138.09: 1 138.09 - 172.61: 1 Dihedral angle restraints: 8077 sinusoidal: 3879 harmonic: 4198 Sorted by residual: dihedral pdb=" O4' U I 26 " pdb=" C1' U I 26 " pdb=" N1 U I 26 " pdb=" C2 U I 26 " ideal model delta sinusoidal sigma weight residual -128.00 44.61 -172.61 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " pdb=" C2 C I 8 " ideal model delta sinusoidal sigma weight residual -128.00 7.31 -135.31 1 1.70e+01 3.46e-03 5.68e+01 dihedral pdb=" CA SER F 160 " pdb=" C SER F 160 " pdb=" N GLN F 161 " pdb=" CA GLN F 161 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 8074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1738 0.055 - 0.111: 266 0.111 - 0.166: 41 0.166 - 0.222: 4 0.222 - 0.277: 3 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C1' A I 27 " pdb=" O4' A I 27 " pdb=" C2' A I 27 " pdb=" N9 A I 27 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1' G I 21 " pdb=" O4' G I 21 " pdb=" C2' G I 21 " pdb=" N9 G I 21 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU B 211 " pdb=" CB LEU B 211 " pdb=" CD1 LEU B 211 " pdb=" CD2 LEU B 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2049 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.058 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 157 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " -0.036 2.00e-02 2.50e+03 1.79e-02 8.82e+00 pdb=" N9 A I 27 " 0.046 2.00e-02 2.50e+03 pdb=" C8 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A I 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A I 27 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A I 27 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " -0.037 2.00e-02 2.50e+03 1.70e-02 8.70e+00 pdb=" N9 G I 21 " 0.044 2.00e-02 2.50e+03 pdb=" C8 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G I 21 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G I 21 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G I 21 " 0.004 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 521 2.70 - 3.25: 13278 3.25 - 3.80: 22147 3.80 - 4.35: 29926 4.35 - 4.90: 47743 Nonbonded interactions: 113615 Sorted by model distance: nonbonded pdb=" OP1 U J 15 " pdb=" OG1 THR D 44 " model vdw 2.146 2.440 nonbonded pdb=" OP1 A I 27 " pdb=" OG SER H 132 " model vdw 2.173 2.440 nonbonded pdb=" O PHE D 98 " pdb=" OG1 THR D 102 " model vdw 2.174 2.440 nonbonded pdb=" OP2 A I 1 " pdb=" OG SER B 37 " model vdw 2.181 2.440 nonbonded pdb=" OP1 C I 31 " pdb=" OH TYR H 297 " model vdw 2.184 2.440 ... (remaining 113610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 16 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 136)) selection = (chain 'D' and (resid 16 through 24 or resid 37 through 136)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.740 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: 0.010 Extract box with map and model: 13.960 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 39.800 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.438 13340 Z= 0.348 Angle : 0.679 24.509 18234 Z= 0.368 Chirality : 0.043 0.277 2052 Planarity : 0.005 0.085 2120 Dihedral : 18.001 172.610 5385 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.33 % Favored : 93.25 % Rotamer: Outliers : 0.62 % Allowed : 13.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1422 helix: 0.38 (0.23), residues: 526 sheet: -1.20 (0.30), residues: 297 loop : -1.60 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 230 HIS 0.005 0.001 HIS H 272 PHE 0.019 0.002 PHE D 74 TYR 0.022 0.002 TYR C 87 ARG 0.005 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 1.357 Fit side-chains REVERT: D 110 ARG cc_start: 0.6254 (mtm180) cc_final: 0.6001 (mtp180) REVERT: B 226 MET cc_start: 0.5894 (tpp) cc_final: 0.5360 (mpp) REVERT: B 283 PHE cc_start: 0.7612 (m-80) cc_final: 0.7367 (m-80) REVERT: H 85 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7656 (pttp) REVERT: H 186 MET cc_start: 0.7880 (tpp) cc_final: 0.7095 (tpp) outliers start: 8 outliers final: 3 residues processed: 222 average time/residue: 0.2550 time to fit residues: 81.5631 Evaluate side-chains 206 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain B residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 57 ASN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 54 ASN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 148 ASN ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13340 Z= 0.447 Angle : 0.729 8.796 18234 Z= 0.388 Chirality : 0.048 0.401 2052 Planarity : 0.005 0.054 2120 Dihedral : 15.795 170.095 2474 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.72 % Favored : 90.86 % Rotamer: Outliers : 3.35 % Allowed : 14.89 % Favored : 81.76 % 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: -1.30 (0.21), residues: 1422 helix: 0.51 (0.22), residues: 524 sheet: -1.22 (0.30), residues: 277 loop : -1.86 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 230 HIS 0.008 0.001 HIS B 17 PHE 0.030 0.002 PHE G 166 TYR 0.022 0.002 TYR H 226 ARG 0.004 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7183 (mt-10) REVERT: F 171 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7479 (mtpt) REVERT: F 180 TYR cc_start: 0.8666 (p90) cc_final: 0.8362 (p90) REVERT: D 26 LYS cc_start: 0.6305 (pptt) cc_final: 0.5951 (pptt) REVERT: D 77 GLU cc_start: 0.6747 (tp30) cc_final: 0.6443 (tp30) REVERT: D 88 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7603 (mm-30) REVERT: D 130 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7376 (mm) REVERT: B 158 GLU cc_start: 0.7838 (mp0) cc_final: 0.7494 (mp0) REVERT: H 28 ASP cc_start: 0.8033 (t0) cc_final: 0.7769 (t0) REVERT: H 40 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5813 (mtp) REVERT: H 149 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.4941 (pt0) REVERT: H 198 GLU cc_start: 0.6966 (mp0) cc_final: 0.6360 (pm20) REVERT: H 283 GLN cc_start: 0.5660 (OUTLIER) cc_final: 0.5286 (pm20) outliers start: 43 outliers final: 25 residues processed: 237 average time/residue: 0.2456 time to fit residues: 83.8633 Evaluate side-chains 220 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS C 71 ASN B 206 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN H 255 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.218 Angle : 0.590 8.075 18234 Z= 0.317 Chirality : 0.043 0.376 2052 Planarity : 0.004 0.050 2120 Dihedral : 15.658 170.729 2474 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.89 % Favored : 92.69 % Rotamer: Outliers : 2.81 % Allowed : 18.00 % Favored : 79.19 % 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: -1.04 (0.22), residues: 1422 helix: 0.78 (0.23), residues: 525 sheet: -1.18 (0.30), residues: 280 loop : -1.74 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 230 HIS 0.004 0.001 HIS F 62 PHE 0.030 0.002 PHE D 120 TYR 0.014 0.001 TYR D 133 ARG 0.005 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: F 171 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7426 (mtpt) REVERT: F 180 TYR cc_start: 0.8569 (p90) cc_final: 0.8320 (p90) REVERT: C 118 LYS cc_start: 0.8100 (mppt) cc_final: 0.7246 (ttpp) REVERT: D 77 GLU cc_start: 0.6786 (tp30) cc_final: 0.6423 (tp30) REVERT: B 158 GLU cc_start: 0.7797 (mp0) cc_final: 0.7452 (mp0) REVERT: H 198 GLU cc_start: 0.6997 (mp0) cc_final: 0.6397 (pm20) REVERT: H 283 GLN cc_start: 0.5726 (OUTLIER) cc_final: 0.5377 (pm20) outliers start: 36 outliers final: 21 residues processed: 247 average time/residue: 0.2457 time to fit residues: 87.4373 Evaluate side-chains 216 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 283 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS C 71 ASN B 206 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13340 Z= 0.333 Angle : 0.649 8.760 18234 Z= 0.346 Chirality : 0.045 0.390 2052 Planarity : 0.004 0.051 2120 Dihedral : 15.661 169.542 2474 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.58 % Favored : 91.00 % Rotamer: Outliers : 4.52 % Allowed : 19.10 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1422 helix: 0.63 (0.22), residues: 528 sheet: -1.32 (0.31), residues: 267 loop : -1.77 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 230 HIS 0.007 0.001 HIS B 17 PHE 0.042 0.002 PHE D 120 TYR 0.017 0.002 TYR C 87 ARG 0.006 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 196 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: G 124 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7848 (mt-10) REVERT: F 81 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7481 (ptp-170) REVERT: F 171 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7536 (mtpt) REVERT: F 180 TYR cc_start: 0.8632 (p90) cc_final: 0.8323 (p90) REVERT: C 118 LYS cc_start: 0.8116 (mppt) cc_final: 0.7251 (ttpp) REVERT: D 63 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: D 77 GLU cc_start: 0.6799 (tp30) cc_final: 0.6414 (tp30) REVERT: D 130 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7379 (mm) REVERT: B 28 MET cc_start: 0.6881 (pmm) cc_final: 0.6674 (pmm) REVERT: B 158 GLU cc_start: 0.7944 (mp0) cc_final: 0.7552 (mp0) REVERT: H 149 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.5219 (pt0) REVERT: H 272 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6976 (t70) REVERT: H 283 GLN cc_start: 0.5693 (OUTLIER) cc_final: 0.5391 (pm20) outliers start: 58 outliers final: 37 residues processed: 238 average time/residue: 0.2474 time to fit residues: 84.9474 Evaluate side-chains 233 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 272 HIS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.0070 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 0.0050 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN C 71 ASN B 106 ASN B 183 GLN H 60 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13340 Z= 0.158 Angle : 0.560 8.871 18234 Z= 0.302 Chirality : 0.042 0.359 2052 Planarity : 0.004 0.045 2120 Dihedral : 15.566 171.552 2474 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.91 % Favored : 93.67 % Rotamer: Outliers : 3.04 % Allowed : 21.04 % Favored : 75.92 % 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: -0.93 (0.22), residues: 1422 helix: 0.88 (0.23), residues: 537 sheet: -1.29 (0.30), residues: 285 loop : -1.62 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 230 HIS 0.005 0.001 HIS F 62 PHE 0.026 0.001 PHE D 120 TYR 0.019 0.001 TYR H 226 ARG 0.005 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 229 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7434 (mt-10) REVERT: G 124 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 138 GLN cc_start: 0.7908 (tt0) cc_final: 0.7490 (mt0) REVERT: F 159 GLU cc_start: 0.5749 (tm-30) cc_final: 0.5347 (tm-30) REVERT: F 171 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7320 (mtpt) REVERT: F 180 TYR cc_start: 0.8475 (p90) cc_final: 0.8170 (p90) REVERT: C 118 LYS cc_start: 0.8040 (mppt) cc_final: 0.7171 (ttpp) REVERT: D 63 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: D 77 GLU cc_start: 0.6690 (tp30) cc_final: 0.6294 (tp30) REVERT: D 130 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7352 (mm) REVERT: B 158 GLU cc_start: 0.7804 (mp0) cc_final: 0.7443 (mp0) REVERT: B 226 MET cc_start: 0.6121 (tpp) cc_final: 0.5366 (tpp) REVERT: H 224 LYS cc_start: 0.7582 (tttt) cc_final: 0.6748 (tmtt) REVERT: H 283 GLN cc_start: 0.5762 (OUTLIER) cc_final: 0.5421 (pm20) outliers start: 39 outliers final: 15 residues processed: 254 average time/residue: 0.2550 time to fit residues: 92.1832 Evaluate side-chains 231 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 283 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS E 135 ASN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 ASN H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 13340 Z= 0.546 Angle : 0.801 10.905 18234 Z= 0.421 Chirality : 0.052 0.428 2052 Planarity : 0.005 0.053 2120 Dihedral : 15.814 170.314 2472 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.56 % Favored : 90.01 % Rotamer: Outliers : 4.36 % Allowed : 21.43 % Favored : 74.20 % 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: -1.48 (0.21), residues: 1422 helix: 0.29 (0.22), residues: 526 sheet: -1.34 (0.31), residues: 265 loop : -1.90 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 230 HIS 0.009 0.001 HIS B 17 PHE 0.032 0.003 PHE D 120 TYR 0.020 0.003 TYR H 155 ARG 0.006 0.001 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7470 (mt-10) REVERT: G 124 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7887 (mt-10) REVERT: F 81 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7488 (ptp-170) REVERT: F 159 GLU cc_start: 0.5958 (tm-30) cc_final: 0.5545 (tm-30) REVERT: F 171 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7442 (mtpt) REVERT: F 180 TYR cc_start: 0.8733 (p90) cc_final: 0.8436 (p90) REVERT: C 118 LYS cc_start: 0.8135 (mppt) cc_final: 0.7269 (ttpp) REVERT: D 63 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7048 (m-80) REVERT: D 77 GLU cc_start: 0.6815 (tp30) cc_final: 0.6423 (tp30) REVERT: D 130 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7226 (mm) REVERT: B 28 MET cc_start: 0.7012 (pmm) cc_final: 0.6708 (pmm) REVERT: B 125 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7426 (p90) REVERT: B 138 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: B 158 GLU cc_start: 0.7980 (mp0) cc_final: 0.7601 (mp0) REVERT: H 149 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5206 (pt0) REVERT: H 224 LYS cc_start: 0.7816 (tttt) cc_final: 0.6936 (tmtt) REVERT: H 283 GLN cc_start: 0.5533 (OUTLIER) cc_final: 0.5112 (mp10) outliers start: 56 outliers final: 37 residues processed: 249 average time/residue: 0.2597 time to fit residues: 92.3829 Evaluate side-chains 240 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 283 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 97 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13340 Z= 0.228 Angle : 0.621 10.522 18234 Z= 0.331 Chirality : 0.045 0.384 2052 Planarity : 0.004 0.044 2120 Dihedral : 15.580 170.305 2472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.54 % Favored : 93.04 % Rotamer: Outliers : 3.12 % Allowed : 22.76 % Favored : 74.12 % 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: -1.21 (0.21), residues: 1422 helix: 0.60 (0.22), residues: 532 sheet: -1.34 (0.31), residues: 265 loop : -1.77 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 230 HIS 0.003 0.001 HIS B 17 PHE 0.029 0.002 PHE D 120 TYR 0.021 0.002 TYR H 223 ARG 0.006 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: G 138 GLN cc_start: 0.7951 (tt0) cc_final: 0.7480 (mt0) REVERT: F 159 GLU cc_start: 0.5744 (tm-30) cc_final: 0.5353 (tm-30) REVERT: F 171 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7392 (mtpt) REVERT: F 180 TYR cc_start: 0.8569 (p90) cc_final: 0.8234 (p90) REVERT: C 118 LYS cc_start: 0.8092 (mppt) cc_final: 0.7186 (ttpp) REVERT: D 63 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: D 77 GLU cc_start: 0.6734 (tp30) cc_final: 0.6335 (tp30) REVERT: D 88 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7509 (mm-30) REVERT: D 130 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7315 (mm) REVERT: B 65 TYR cc_start: 0.7332 (p90) cc_final: 0.6881 (p90) REVERT: B 158 GLU cc_start: 0.7885 (mp0) cc_final: 0.7462 (mp0) REVERT: B 226 MET cc_start: 0.5991 (tpp) cc_final: 0.5478 (tpp) REVERT: H 119 MET cc_start: 0.7936 (ppp) cc_final: 0.7605 (ptm) REVERT: H 224 LYS cc_start: 0.7661 (tttt) cc_final: 0.6793 (tmtt) REVERT: H 283 GLN cc_start: 0.5492 (OUTLIER) cc_final: 0.5050 (mp10) outliers start: 40 outliers final: 28 residues processed: 245 average time/residue: 0.2652 time to fit residues: 92.8848 Evaluate side-chains 231 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.0470 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS E 135 ASN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13340 Z= 0.198 Angle : 0.601 10.553 18234 Z= 0.319 Chirality : 0.044 0.392 2052 Planarity : 0.004 0.043 2120 Dihedral : 15.441 171.188 2472 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 2.96 % Allowed : 23.15 % Favored : 73.89 % 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: -1.07 (0.22), residues: 1422 helix: 0.70 (0.23), residues: 531 sheet: -1.26 (0.30), residues: 275 loop : -1.67 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 230 HIS 0.004 0.001 HIS B 17 PHE 0.025 0.002 PHE D 120 TYR 0.018 0.001 TYR H 226 ARG 0.005 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.408 Fit side-chains REVERT: E 124 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7458 (mt-10) REVERT: G 124 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7762 (mt-10) REVERT: G 138 GLN cc_start: 0.7911 (tt0) cc_final: 0.7485 (mt0) REVERT: F 27 MET cc_start: 0.5751 (tpt) cc_final: 0.5370 (tpt) REVERT: F 92 GLN cc_start: 0.7213 (pm20) cc_final: 0.6886 (pm20) REVERT: F 159 GLU cc_start: 0.5705 (tm-30) cc_final: 0.5310 (tm-30) REVERT: F 171 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7330 (mtpt) REVERT: F 180 TYR cc_start: 0.8531 (p90) cc_final: 0.8216 (p90) REVERT: D 63 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: D 76 ASP cc_start: 0.5854 (m-30) cc_final: 0.5571 (m-30) REVERT: D 77 GLU cc_start: 0.6755 (tp30) cc_final: 0.6353 (tp30) REVERT: D 88 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 130 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 158 GLU cc_start: 0.7806 (mp0) cc_final: 0.7445 (mp0) REVERT: H 119 MET cc_start: 0.7874 (ppp) cc_final: 0.7574 (ptm) REVERT: H 224 LYS cc_start: 0.7657 (tttt) cc_final: 0.6758 (tmtt) REVERT: H 283 GLN cc_start: 0.5478 (OUTLIER) cc_final: 0.5091 (mp10) outliers start: 38 outliers final: 27 residues processed: 236 average time/residue: 0.2624 time to fit residues: 88.0474 Evaluate side-chains 233 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.0050 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13340 Z= 0.203 Angle : 0.606 10.631 18234 Z= 0.320 Chirality : 0.044 0.377 2052 Planarity : 0.004 0.047 2120 Dihedral : 15.399 171.147 2472 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Rotamer: Outliers : 2.88 % Allowed : 23.15 % Favored : 73.97 % 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: -1.09 (0.22), residues: 1422 helix: 0.64 (0.23), residues: 535 sheet: -1.51 (0.30), residues: 297 loop : -1.51 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.003 0.001 HIS F 62 PHE 0.025 0.002 PHE D 120 TYR 0.018 0.001 TYR D 133 ARG 0.009 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7527 (mt-10) REVERT: G 27 MET cc_start: 0.6975 (ttt) cc_final: 0.6759 (ttt) REVERT: G 124 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7820 (mt-10) REVERT: G 138 GLN cc_start: 0.7879 (tt0) cc_final: 0.7673 (mt0) REVERT: F 171 LYS cc_start: 0.7528 (mtpt) cc_final: 0.7274 (mtpt) REVERT: F 180 TYR cc_start: 0.8521 (p90) cc_final: 0.8223 (p90) REVERT: C 118 LYS cc_start: 0.8048 (mppt) cc_final: 0.7177 (ttpp) REVERT: D 63 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: D 77 GLU cc_start: 0.6732 (tp30) cc_final: 0.6337 (tp30) REVERT: D 88 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7472 (mm-30) REVERT: D 130 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7272 (mm) REVERT: B 65 TYR cc_start: 0.7486 (p90) cc_final: 0.6292 (p90) REVERT: B 158 GLU cc_start: 0.7788 (mp0) cc_final: 0.7579 (mp0) REVERT: H 119 MET cc_start: 0.7853 (ppp) cc_final: 0.7574 (ptm) REVERT: H 224 LYS cc_start: 0.7668 (tttt) cc_final: 0.6765 (tmtt) REVERT: H 283 GLN cc_start: 0.5529 (OUTLIER) cc_final: 0.5140 (mp10) outliers start: 37 outliers final: 27 residues processed: 240 average time/residue: 0.2666 time to fit residues: 90.8192 Evaluate side-chains 227 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13340 Z= 0.201 Angle : 0.611 14.108 18234 Z= 0.321 Chirality : 0.044 0.392 2052 Planarity : 0.004 0.048 2120 Dihedral : 15.359 171.607 2472 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.10 % Favored : 92.55 % Rotamer: Outliers : 2.34 % Allowed : 24.16 % Favored : 73.50 % 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: -1.05 (0.22), residues: 1422 helix: 0.65 (0.23), residues: 535 sheet: -1.45 (0.30), residues: 298 loop : -1.48 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.003 0.001 HIS B 17 PHE 0.027 0.002 PHE D 120 TYR 0.025 0.001 TYR C 87 ARG 0.010 0.000 ARG H 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 MET cc_start: 0.7028 (ttt) cc_final: 0.6689 (ttt) REVERT: G 124 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7771 (mt-10) REVERT: F 180 TYR cc_start: 0.8518 (p90) cc_final: 0.8212 (p90) REVERT: C 118 LYS cc_start: 0.8017 (mppt) cc_final: 0.7165 (ttpp) REVERT: D 51 LEU cc_start: 0.7957 (mp) cc_final: 0.7671 (mt) REVERT: D 63 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: D 77 GLU cc_start: 0.6715 (tp30) cc_final: 0.6285 (tp30) REVERT: D 130 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7167 (mm) REVERT: D 133 TYR cc_start: 0.7581 (m-80) cc_final: 0.7367 (m-80) REVERT: B 65 TYR cc_start: 0.7445 (p90) cc_final: 0.6246 (p90) REVERT: H 119 MET cc_start: 0.7804 (ppp) cc_final: 0.7557 (ptm) REVERT: H 224 LYS cc_start: 0.7619 (tttt) cc_final: 0.6732 (tmtt) REVERT: H 283 GLN cc_start: 0.5595 (OUTLIER) cc_final: 0.5238 (mp10) outliers start: 30 outliers final: 25 residues processed: 231 average time/residue: 0.2686 time to fit residues: 89.2174 Evaluate side-chains 232 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136638 restraints weight = 21518.256| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.27 r_work: 0.3658 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13340 Z= 0.349 Angle : 0.707 16.253 18234 Z= 0.369 Chirality : 0.048 0.408 2052 Planarity : 0.005 0.052 2120 Dihedral : 15.435 169.197 2472 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.72 % Favored : 90.93 % Rotamer: Outliers : 2.81 % Allowed : 23.77 % Favored : 73.42 % 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: -1.24 (0.22), residues: 1422 helix: 0.38 (0.22), residues: 536 sheet: -1.26 (0.31), residues: 275 loop : -1.65 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 230 HIS 0.006 0.001 HIS B 17 PHE 0.021 0.002 PHE D 74 TYR 0.026 0.002 TYR C 87 ARG 0.010 0.001 ARG H 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.13 seconds wall clock time: 54 minutes 58.69 seconds (3298.69 seconds total)