Starting phenix.real_space_refine on Fri Jan 19 23:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/01_2024/8do6_27593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/01_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_27593/01_2024/8do6_27593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/01_2024/8do6_27593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/01_2024/8do6_27593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do6_27593/01_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 7.10, per 1000 atoms: 0.55 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: 5.85 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: 4.68 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: 4.60 Time building geometry restraints manager: 6.25 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: 7681 34.52 - 69.04: 288 69.04 - 103.57: 38 103.57 - 138.09: 1 138.09 - 172.61: 1 Dihedral angle restraints: 8009 sinusoidal: 3811 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 8006 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: 4.640 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: 26.760 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 39.930 Find NCS groups from input model: 0.540 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.820 ------------------------------------------------------------------------------- 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 : 17.607 172.610 5317 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 : 1.461 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: 0.2600 time to fit residues: 83.1918 Evaluate side-chains 206 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 13340 Z= 0.485 Angle : 0.754 8.942 18234 Z= 0.401 Chirality : 0.049 0.414 2052 Planarity : 0.005 0.055 2120 Dihedral : 14.892 170.997 2406 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.00 % Favored : 90.58 % Rotamer: Outliers : 3.43 % Allowed : 14.96 % Favored : 81.61 % 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: -1.35 (0.21), residues: 1422 helix: 0.46 (0.22), residues: 524 sheet: -1.26 (0.30), residues: 277 loop : -1.89 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 230 HIS 0.009 0.001 HIS B 17 PHE 0.030 0.002 PHE G 166 TYR 0.023 0.002 TYR H 226 ARG 0.004 0.000 ARG B 191 *********************** 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 251 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7187 (mt-10) REVERT: G 138 GLN cc_start: 0.8030 (tt0) cc_final: 0.7790 (tt0) REVERT: F 137 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8355 (ttp-110) REVERT: F 171 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7496 (mtpt) REVERT: F 180 TYR cc_start: 0.8688 (p90) cc_final: 0.8383 (p90) REVERT: D 77 GLU cc_start: 0.6764 (tp30) cc_final: 0.6463 (tp30) REVERT: D 88 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7605 (mm-30) REVERT: D 130 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7362 (mm) REVERT: B 158 GLU cc_start: 0.7845 (mp0) cc_final: 0.7516 (mp0) REVERT: H 28 ASP cc_start: 0.8027 (t0) cc_final: 0.7769 (t0) REVERT: H 40 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5927 (mtp) REVERT: H 149 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.4938 (pt0) REVERT: H 198 GLU cc_start: 0.6975 (mp0) cc_final: 0.6371 (pm20) REVERT: H 283 GLN cc_start: 0.5642 (OUTLIER) cc_final: 0.5259 (pm20) outliers start: 44 outliers final: 27 residues processed: 234 average time/residue: 0.2460 time to fit residues: 83.5159 Evaluate side-chains 221 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 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 179 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain F residue 137 ARG 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: 0.6980 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 D 24 ASN B 183 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13340 Z= 0.186 Angle : 0.573 7.998 18234 Z= 0.309 Chirality : 0.043 0.373 2052 Planarity : 0.004 0.048 2120 Dihedral : 14.657 171.724 2406 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.26 % Favored : 93.32 % Rotamer: Outliers : 2.73 % Allowed : 17.85 % Favored : 79.42 % 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: -0.99 (0.22), residues: 1422 helix: 0.76 (0.23), residues: 537 sheet: -1.16 (0.30), residues: 279 loop : -1.68 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 230 HIS 0.004 0.001 HIS F 62 PHE 0.029 0.001 PHE D 120 TYR 0.015 0.001 TYR H 226 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 257 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: F 171 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7418 (mtpt) REVERT: F 180 TYR cc_start: 0.8551 (p90) cc_final: 0.8336 (p90) REVERT: D 77 GLU cc_start: 0.6774 (tp30) cc_final: 0.6413 (tp30) REVERT: B 158 GLU cc_start: 0.7802 (mp0) cc_final: 0.7472 (mp0) REVERT: B 226 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.6041 (tpp) REVERT: H 198 GLU cc_start: 0.6979 (mp0) cc_final: 0.6383 (pm20) REVERT: H 283 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.5451 (pm20) outliers start: 35 outliers final: 20 residues processed: 242 average time/residue: 0.2625 time to fit residues: 91.2302 Evaluate side-chains 216 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 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 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 D residue 84 LYS 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 138 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain H residue 150 LYS 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: 0.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 183 GLN B 206 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: 0.7647 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13340 Z= 0.209 Angle : 0.572 8.947 18234 Z= 0.307 Chirality : 0.043 0.367 2052 Planarity : 0.004 0.048 2120 Dihedral : 14.549 171.112 2406 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.31 % Favored : 92.26 % Rotamer: Outliers : 3.90 % Allowed : 18.55 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.22), residues: 1422 helix: 0.91 (0.23), residues: 529 sheet: -1.10 (0.31), residues: 277 loop : -1.68 (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 0.039 0.002 PHE D 120 TYR 0.016 0.001 TYR C 87 ARG 0.005 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 257 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 207 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 91 ILE cc_start: 0.8837 (tp) cc_final: 0.8623 (tt) REVERT: G 124 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7769 (mt-10) REVERT: F 81 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7504 (ptp-170) REVERT: F 124 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7458 (mm-30) REVERT: F 159 GLU cc_start: 0.5748 (tm-30) cc_final: 0.5523 (tm-30) REVERT: F 180 TYR cc_start: 0.8558 (p90) cc_final: 0.8253 (p90) REVERT: C 118 LYS cc_start: 0.8096 (mppt) cc_final: 0.7225 (ttpp) REVERT: D 77 GLU cc_start: 0.6765 (tp30) cc_final: 0.6305 (tp30) REVERT: D 84 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.5754 (tptt) REVERT: D 130 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7372 (mm) REVERT: B 158 GLU cc_start: 0.7836 (mp0) cc_final: 0.7440 (mp0) REVERT: H 283 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.5403 (pm20) outliers start: 50 outliers final: 27 residues processed: 242 average time/residue: 0.2621 time to fit residues: 90.5243 Evaluate side-chains 227 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 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 D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS 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 103 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 30 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 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: 0.7716 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13340 Z= 0.301 Angle : 0.634 8.274 18234 Z= 0.339 Chirality : 0.045 0.389 2052 Planarity : 0.004 0.051 2120 Dihedral : 14.625 170.021 2404 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.02 % Favored : 91.56 % Rotamer: Outliers : 4.05 % Allowed : 20.03 % 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: -1.14 (0.21), residues: 1422 helix: 0.69 (0.22), residues: 530 sheet: -1.30 (0.30), residues: 277 loop : -1.76 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 230 HIS 0.006 0.001 HIS B 17 PHE 0.032 0.002 PHE D 120 TYR 0.017 0.002 TYR C 87 ARG 0.005 0.000 ARG H 64 *********************** 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 262 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 210 time to evaluate : 1.515 Fit side-chains REVERT: E 91 ILE cc_start: 0.8853 (tp) cc_final: 0.8641 (tt) REVERT: G 124 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7816 (mt-10) REVERT: F 81 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7509 (ptp-170) REVERT: F 159 GLU cc_start: 0.5850 (tm-30) cc_final: 0.5457 (tm-30) REVERT: F 180 TYR cc_start: 0.8663 (p90) cc_final: 0.8336 (p90) REVERT: C 118 LYS cc_start: 0.8105 (mppt) cc_final: 0.7225 (ttpp) REVERT: D 63 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: D 77 GLU cc_start: 0.6801 (tp30) cc_final: 0.6358 (tp30) REVERT: D 84 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.5578 (tptt) REVERT: D 88 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7554 (mm-30) REVERT: D 130 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7347 (mm) REVERT: D 133 TYR cc_start: 0.7637 (m-80) cc_final: 0.7404 (m-10) REVERT: B 158 GLU cc_start: 0.7876 (mp0) cc_final: 0.7412 (mp0) REVERT: B 226 MET cc_start: 0.6288 (tpp) cc_final: 0.5752 (tpp) REVERT: H 283 GLN cc_start: 0.5669 (OUTLIER) cc_final: 0.5387 (pm20) outliers start: 52 outliers final: 37 residues processed: 246 average time/residue: 0.2603 time to fit residues: 92.1676 Evaluate side-chains 237 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS 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 138 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 THR 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 B residue 267 SER Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 36 SER 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 195 VAL Chi-restraints excluded: chain H residue 207 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 117 optimal weight: 0.0000 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- 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** B 106 ASN B 206 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13340 Z= 0.225 Angle : 0.595 9.230 18234 Z= 0.318 Chirality : 0.044 0.376 2052 Planarity : 0.004 0.050 2120 Dihedral : 14.565 171.122 2404 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.17 % Favored : 92.41 % Rotamer: Outliers : 4.36 % Allowed : 20.03 % Favored : 75.60 % 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: -0.98 (0.22), residues: 1422 helix: 0.83 (0.23), residues: 532 sheet: -1.19 (0.31), residues: 275 loop : -1.68 (0.23), residues: 615 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 0.027 0.001 PHE D 120 TYR 0.016 0.001 TYR H 226 ARG 0.005 0.000 ARG H 64 *********************** 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 263 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 207 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7457 (mt-10) REVERT: G 138 GLN cc_start: 0.7866 (tt0) cc_final: 0.7463 (mt0) REVERT: F 81 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7504 (ptp-170) REVERT: F 159 GLU cc_start: 0.5769 (tm-30) cc_final: 0.5376 (tm-30) REVERT: F 180 TYR cc_start: 0.8563 (p90) cc_final: 0.8245 (p90) REVERT: C 118 LYS cc_start: 0.8055 (mppt) cc_final: 0.7179 (ttpp) REVERT: D 63 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: D 77 GLU cc_start: 0.6777 (tp30) cc_final: 0.6326 (tp30) REVERT: D 130 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7309 (mm) REVERT: D 133 TYR cc_start: 0.7519 (m-80) cc_final: 0.7263 (m-10) REVERT: B 158 GLU cc_start: 0.7855 (mp0) cc_final: 0.7359 (mp0) REVERT: H 119 MET cc_start: 0.7940 (ppp) cc_final: 0.7620 (ptm) REVERT: H 224 LYS cc_start: 0.7663 (tttt) cc_final: 0.6853 (tmtt) REVERT: H 283 GLN cc_start: 0.5660 (OUTLIER) cc_final: 0.5366 (pm20) outliers start: 56 outliers final: 37 residues processed: 245 average time/residue: 0.2639 time to fit residues: 92.8164 Evaluate side-chains 236 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 32 ASP 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 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 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS 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 179 MET 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 B residue 267 SER Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 36 SER 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 195 VAL Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 228 ASP 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: 1.9990 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** B 206 GLN H 60 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13340 Z= 0.208 Angle : 0.594 10.555 18234 Z= 0.315 Chirality : 0.044 0.371 2052 Planarity : 0.004 0.051 2120 Dihedral : 14.530 171.103 2404 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.31 % Favored : 92.26 % Rotamer: Outliers : 3.82 % Allowed : 21.28 % Favored : 74.90 % 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: -0.91 (0.22), residues: 1422 helix: 0.90 (0.23), residues: 532 sheet: -1.37 (0.31), residues: 282 loop : -1.54 (0.23), residues: 608 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 0.001 PHE D 120 TYR 0.017 0.001 TYR H 226 ARG 0.004 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 261 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7478 (mt-10) REVERT: F 81 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7499 (ptp-170) REVERT: F 159 GLU cc_start: 0.5687 (tm-30) cc_final: 0.5303 (tm-30) REVERT: F 180 TYR cc_start: 0.8568 (p90) cc_final: 0.8231 (p90) REVERT: C 118 LYS cc_start: 0.8040 (mppt) cc_final: 0.7170 (ttpp) REVERT: D 63 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: D 77 GLU cc_start: 0.6772 (tp30) cc_final: 0.6323 (tp30) REVERT: D 130 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7375 (mm) REVERT: D 133 TYR cc_start: 0.7376 (m-80) cc_final: 0.7156 (m-10) REVERT: B 158 GLU cc_start: 0.7826 (mp0) cc_final: 0.7351 (mp0) REVERT: B 226 MET cc_start: 0.6223 (tpp) cc_final: 0.5631 (tpp) REVERT: H 60 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7441 (mm-40) REVERT: H 119 MET cc_start: 0.7941 (ppp) cc_final: 0.7662 (ptm) REVERT: H 224 LYS cc_start: 0.7670 (tttt) cc_final: 0.6807 (tmtt) REVERT: H 283 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.5272 (pm20) outliers start: 49 outliers final: 35 residues processed: 249 average time/residue: 0.2630 time to fit residues: 93.9981 Evaluate side-chains 231 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 10 THR 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 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS 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 179 MET 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 B residue 267 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 207 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 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: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 60 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13340 Z= 0.306 Angle : 0.647 10.548 18234 Z= 0.342 Chirality : 0.046 0.385 2052 Planarity : 0.004 0.053 2120 Dihedral : 14.573 169.717 2404 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.23 % Favored : 91.35 % Rotamer: Outliers : 3.98 % Allowed : 21.28 % Favored : 74.75 % 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: -1.10 (0.22), residues: 1422 helix: 0.65 (0.22), residues: 536 sheet: -1.24 (0.31), residues: 272 loop : -1.72 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 230 HIS 0.006 0.001 HIS B 17 PHE 0.025 0.002 PHE D 120 TYR 0.023 0.002 TYR C 87 ARG 0.007 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 246 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 195 time to evaluate : 1.467 Fit side-chains REVERT: E 124 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 42 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8309 (ttpt) REVERT: F 81 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7506 (ptp-170) REVERT: F 159 GLU cc_start: 0.5771 (tm-30) cc_final: 0.5380 (tm-30) REVERT: F 180 TYR cc_start: 0.8660 (p90) cc_final: 0.8320 (p90) REVERT: C 118 LYS cc_start: 0.8044 (mppt) cc_final: 0.7168 (ttpp) REVERT: D 63 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: D 77 GLU cc_start: 0.6801 (tp30) cc_final: 0.6329 (tp30) REVERT: D 84 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.5610 (tptt) REVERT: D 130 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7215 (mm) REVERT: D 133 TYR cc_start: 0.7737 (m-80) cc_final: 0.7406 (m-80) REVERT: B 158 GLU cc_start: 0.7870 (mp0) cc_final: 0.7394 (mp0) REVERT: H 119 MET cc_start: 0.8059 (ppp) cc_final: 0.7775 (ptm) REVERT: H 224 LYS cc_start: 0.7674 (tttt) cc_final: 0.6796 (tmtt) REVERT: H 283 GLN cc_start: 0.5539 (OUTLIER) cc_final: 0.5131 (mp10) outliers start: 51 outliers final: 35 residues processed: 233 average time/residue: 0.2672 time to fit residues: 88.6351 Evaluate side-chains 228 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 11 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 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 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS 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 179 MET 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 B residue 267 SER 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 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 207 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2149 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= 0.202 Angle : 0.604 10.864 18234 Z= 0.319 Chirality : 0.044 0.371 2052 Planarity : 0.004 0.050 2120 Dihedral : 14.421 171.549 2404 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.75 % Favored : 92.90 % Rotamer: Outliers : 3.20 % Allowed : 22.29 % Favored : 74.51 % 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: -1.01 (0.22), residues: 1422 helix: 0.77 (0.23), residues: 535 sheet: -1.40 (0.30), residues: 283 loop : -1.57 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.004 0.001 HIS B 17 PHE 0.020 0.001 PHE D 120 TYR 0.019 0.001 TYR C 87 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 247 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7506 (mt-10) REVERT: G 138 GLN cc_start: 0.7923 (tt0) cc_final: 0.7516 (mt0) REVERT: F 159 GLU cc_start: 0.5642 (tm-30) cc_final: 0.5254 (tm-30) REVERT: F 180 TYR cc_start: 0.8556 (p90) cc_final: 0.8238 (p90) REVERT: C 118 LYS cc_start: 0.8051 (mppt) cc_final: 0.7186 (ttpp) REVERT: D 63 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: D 77 GLU cc_start: 0.6773 (tp30) cc_final: 0.6337 (tp30) REVERT: D 130 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7310 (mm) REVERT: B 158 GLU cc_start: 0.7839 (mp0) cc_final: 0.7328 (mp0) REVERT: B 226 MET cc_start: 0.6141 (tpp) cc_final: 0.5685 (mpp) REVERT: H 119 MET cc_start: 0.7906 (ppp) cc_final: 0.7666 (ptm) REVERT: H 224 LYS cc_start: 0.7632 (tttt) cc_final: 0.6742 (tmtt) REVERT: H 283 GLN cc_start: 0.5507 (OUTLIER) cc_final: 0.5111 (mp10) outliers start: 41 outliers final: 33 residues processed: 234 average time/residue: 0.2875 time to fit residues: 95.4650 Evaluate side-chains 233 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 155 ASN Chi-restraints excluded: chain F residue 10 THR 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 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 130 LEU 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 179 MET 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 B residue 267 SER 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 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 207 ASP 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 138 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 0.0870 chunk 133 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 92 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13340 Z= 0.171 Angle : 0.584 11.224 18234 Z= 0.309 Chirality : 0.043 0.386 2052 Planarity : 0.004 0.050 2120 Dihedral : 14.316 171.778 2404 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.47 % Favored : 93.18 % Rotamer: Outliers : 2.65 % Allowed : 22.92 % Favored : 74.43 % 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: -0.92 (0.22), residues: 1422 helix: 0.86 (0.23), residues: 537 sheet: -1.40 (0.30), residues: 295 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 0.017 0.001 PHE D 120 TYR 0.018 0.001 TYR H 226 ARG 0.008 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 249 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7532 (mt-10) REVERT: G 138 GLN cc_start: 0.7887 (tt0) cc_final: 0.7508 (mt0) REVERT: F 159 GLU cc_start: 0.5665 (tm-30) cc_final: 0.5426 (tm-30) REVERT: F 180 TYR cc_start: 0.8531 (p90) cc_final: 0.8217 (p90) REVERT: C 118 LYS cc_start: 0.8027 (mppt) cc_final: 0.7173 (ttpp) REVERT: D 63 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: D 73 GLU cc_start: 0.7532 (tp30) cc_final: 0.7261 (mt-10) REVERT: D 77 GLU cc_start: 0.6672 (tp30) cc_final: 0.6237 (tp30) REVERT: D 130 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7325 (mm) REVERT: B 158 GLU cc_start: 0.7778 (mp0) cc_final: 0.7358 (mp0) REVERT: B 226 MET cc_start: 0.6143 (tpp) cc_final: 0.5266 (mpp) REVERT: H 224 LYS cc_start: 0.7597 (tttt) cc_final: 0.6721 (tmtt) REVERT: H 283 GLN cc_start: 0.5543 (OUTLIER) cc_final: 0.5177 (mp10) outliers start: 34 outliers final: 25 residues processed: 236 average time/residue: 0.2621 time to fit residues: 90.8777 Evaluate side-chains 229 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 155 ASN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 120 GLU 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 84 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 24 SER 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 B residue 267 SER 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 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: 5.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 60 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142060 restraints weight = 21383.444| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.27 r_work: 0.3738 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13340 Z= 0.210 Angle : 0.608 12.105 18234 Z= 0.320 Chirality : 0.044 0.371 2052 Planarity : 0.004 0.053 2120 Dihedral : 14.297 170.959 2402 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.03 % Favored : 92.62 % Rotamer: Outliers : 2.73 % Allowed : 23.15 % 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: -0.92 (0.22), residues: 1422 helix: 0.88 (0.23), residues: 531 sheet: -1.39 (0.30), residues: 295 loop : -1.51 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.004 0.001 HIS B 17 PHE 0.017 0.001 PHE D 16 TYR 0.017 0.001 TYR H 226 ARG 0.010 0.000 ARG H 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3076.21 seconds wall clock time: 58 minutes 5.74 seconds (3485.74 seconds total)