Starting phenix.real_space_refine on Wed Aug 7 20:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/08_2024/8qyl_18757.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/08_2024/8qyl_18757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/08_2024/8qyl_18757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/08_2024/8qyl_18757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/08_2024/8qyl_18757.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/08_2024/8qyl_18757.cif" } resolution = 2.67 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= 0.009 sd= 0.127 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: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 13337 2.51 5 N 3571 2.21 5 O 3958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "I TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 182": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20997 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1791 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 220} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1916 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1880 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 233} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1760 Unusual residues: {'ACE': 1} Classifications: {'peptide': 229, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1898 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "H" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "I" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2128 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1956 Unusual residues: {'ACE': 1} Classifications: {'peptide': 249, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Chain: "K" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 2 Time building chain proxies: 11.64, per 1000 atoms: 0.55 Number of scatterers: 20997 At special positions: 0 Unit cell: (125.126, 142.15, 145.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 131 16.00 O 3958 8.00 N 3571 7.00 C 13337 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: 7.67 Conformation dependent library (CDL) restraints added in 4.0 seconds 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 24 sheets defined 41.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.862A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.669A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.664A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.533A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.738A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.627A pdb=" N LEU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.681A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 249 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.614A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.564A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 60' Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.547A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.943A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.106A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 221 through 241 removed outlier: 4.131A pdb=" N LYS C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.549A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 104 Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.830A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 237 removed outlier: 3.702A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.737A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 77 through 99 removed outlier: 3.710A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.971A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 179 removed outlier: 3.979A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.616A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 removed outlier: 3.628A pdb=" N SER F 34 " --> pdb=" O VAL F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 removed outlier: 3.555A pdb=" N TYR F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.958A pdb=" N GLU F 184 " --> pdb=" O GLN F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.319A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.556A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 4.074A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 35' Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 126 removed outlier: 3.650A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.528A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 206 removed outlier: 3.678A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 47 through 54 removed outlier: 4.301A pdb=" N SER H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 71 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.684A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.844A pdb=" N ILE H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 32 through 45 Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.873A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 87 Processing helix chain 'I' and resid 142 through 154 removed outlier: 4.793A pdb=" N TYR I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN I 148 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.866A pdb=" N LEU I 184 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 227 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 removed outlier: 3.550A pdb=" N SER I 255 " --> pdb=" O PRO I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 279 removed outlier: 3.586A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR I 279 " --> pdb=" O LYS I 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 66 through 70 removed outlier: 4.110A pdb=" N THR J 69 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU J 70 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 66 through 70' Processing helix chain 'J' and resid 98 through 114 removed outlier: 3.536A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 129 No H-bonds generated for 'chain 'J' and resid 127 through 129' Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.599A pdb=" N ARG J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 159 removed outlier: 3.543A pdb=" N GLN J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 197 Processing helix chain 'J' and resid 213 through 229 removed outlier: 4.028A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 92 through 114 Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.547A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 184 removed outlier: 3.764A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 207 removed outlier: 3.585A pdb=" N GLY K 205 " --> pdb=" O ALA K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'L' and resid 56 through 79 removed outlier: 3.650A pdb=" N GLN L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 98 removed outlier: 4.202A pdb=" N LYS L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 154 removed outlier: 4.389A pdb=" N MET L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.669A pdb=" N GLY A 43 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.546A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 137 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.503A pdb=" N ILE B 37 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.802A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.652A pdb=" N GLU D 216 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 80 removed outlier: 3.805A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 145 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.586A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'G' and resid 5 through 6 removed outlier: 6.079A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.130A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.539A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AB9, first strand: chain 'J' and resid 1 through 4 removed outlier: 6.981A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 1 through 4 removed outlier: 6.981A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 140 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 41 through 42 removed outlier: 6.333A pdb=" N ILE K 84 " --> pdb=" O ILE K 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 41 through 42 Processing sheet with id=AC4, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.516A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 252 through 261 removed outlier: 6.598A pdb=" N THR L 199 " --> pdb=" O UNK K 255 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N UNK K 257 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR L 197 " --> pdb=" O UNK K 257 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N UNK K 259 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE L 195 " --> pdb=" O UNK K 259 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL L 185 " --> pdb=" O LEU L 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 42 through 44 1061 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.28 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3519 1.30 - 1.43: 5248 1.43 - 1.56: 12407 1.56 - 1.69: 0 1.69 - 1.82: 203 Bond restraints: 21377 Sorted by residual: bond pdb=" N VAL J 3 " pdb=" CA VAL J 3 " ideal model delta sigma weight residual 1.461 1.483 -0.023 9.10e-03 1.21e+04 6.30e+00 bond pdb=" N PHE D 2 " pdb=" CA PHE D 2 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.29e-02 6.01e+03 5.00e+00 bond pdb=" N ARG E 3 " pdb=" CA ARG E 3 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.49e+00 bond pdb=" N PHE E 2 " pdb=" CA PHE E 2 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.26e-02 6.30e+03 3.14e+00 bond pdb=" N PHE J 2 " pdb=" CA PHE J 2 " ideal model delta sigma weight residual 1.459 1.480 -0.020 1.24e-02 6.50e+03 2.65e+00 ... (remaining 21372 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.54: 387 105.54 - 112.66: 11192 112.66 - 119.78: 7143 119.78 - 126.89: 9956 126.89 - 134.01: 200 Bond angle restraints: 28878 Sorted by residual: angle pdb=" CA PHE E 2 " pdb=" CB PHE E 2 " pdb=" CG PHE E 2 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.34e+01 angle pdb=" N ARG E 3 " pdb=" CA ARG E 3 " pdb=" C ARG E 3 " ideal model delta sigma weight residual 113.17 108.77 4.40 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C ACE D 0 " pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 121.70 131.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C ARG E 3 " pdb=" N ASN E 4 " pdb=" CA ASN E 4 " ideal model delta sigma weight residual 120.31 115.54 4.77 1.52e+00 4.33e-01 9.84e+00 angle pdb=" N GLU L 151 " pdb=" CA GLU L 151 " pdb=" CB GLU L 151 " ideal model delta sigma weight residual 110.12 114.67 -4.55 1.47e+00 4.63e-01 9.57e+00 ... (remaining 28873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11821 17.89 - 35.78: 952 35.78 - 53.67: 136 53.67 - 71.57: 44 71.57 - 89.46: 21 Dihedral angle restraints: 12974 sinusoidal: 5176 harmonic: 7798 Sorted by residual: dihedral pdb=" CH3 ACE E 0 " pdb=" C ACE E 0 " pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sinusoidal sigma weight residual 180.00 -153.29 -26.71 1 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CH3 ACE J 0 " pdb=" C ACE J 0 " pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sinusoidal sigma weight residual -180.00 -154.95 -25.05 1 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.33 -19.67 1 5.00e+00 4.00e-02 2.24e+01 ... (remaining 12971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2391 0.043 - 0.087: 643 0.087 - 0.130: 223 0.130 - 0.173: 13 0.173 - 0.217: 2 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA VAL J 3 " pdb=" N VAL J 3 " pdb=" C VAL J 3 " pdb=" CB VAL J 3 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR D 113 " pdb=" CA THR D 113 " pdb=" OG1 THR D 113 " pdb=" CG2 THR D 113 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA GLN I 208 " pdb=" N GLN I 208 " pdb=" C GLN I 208 " pdb=" CB GLN I 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 3269 not shown) Planarity restraints: 3698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.042 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" O ACE J 0 " 0.023 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.117 2.00e-02 2.50e+03 pdb=" N MET J 1 " 0.207 2.00e-02 2.50e+03 pdb=" CA MET J 1 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE E 0 " -0.034 2.00e-02 2.50e+03 1.23e-01 1.91e+02 pdb=" O ACE E 0 " -0.011 2.00e-02 2.50e+03 pdb=" CH3 ACE E 0 " 0.106 2.00e-02 2.50e+03 pdb=" N MET E 1 " -0.206 2.00e-02 2.50e+03 pdb=" CA MET E 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " 0.021 2.00e-02 2.50e+03 8.77e-02 9.62e+01 pdb=" O ACE D 0 " 0.007 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " -0.074 2.00e-02 2.50e+03 pdb=" N MET D 1 " 0.149 2.00e-02 2.50e+03 pdb=" CA MET D 1 " -0.102 2.00e-02 2.50e+03 ... (remaining 3695 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3054 2.76 - 3.30: 18261 3.30 - 3.83: 32284 3.83 - 4.37: 38546 4.37 - 4.90: 70238 Nonbonded interactions: 162383 Sorted by model distance: nonbonded pdb=" NH1 ARG A 143 " pdb=" O PRO A 144 " model vdw 2.225 3.120 nonbonded pdb=" NH1 ARG A 84 " pdb=" OD1 ASP G 120 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP F 203 " pdb=" NZ LYS F 206 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR G 67 " pdb=" OE2 GLU G 216 " model vdw 2.265 3.040 nonbonded pdb=" O UNK K 249 " pdb=" NE2 GLN L 169 " model vdw 2.269 3.120 ... (remaining 162378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 55.250 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 : 0.003 0.035 21377 Z= 0.220 Angle : 0.519 9.989 28878 Z= 0.280 Chirality : 0.044 0.217 3272 Planarity : 0.006 0.129 3698 Dihedral : 13.753 89.457 7950 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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 (0.16), residues: 2629 helix: 2.30 (0.17), residues: 951 sheet: 0.50 (0.21), residues: 541 loop : -0.84 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP F 216 HIS 0.004 0.001 HIS D 73 PHE 0.020 0.001 PHE L 69 TYR 0.013 0.001 TYR B 136 ARG 0.005 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.511 Fit side-chains REVERT: C 102 VAL cc_start: 0.8636 (t) cc_final: 0.8413 (p) REVERT: J 96 LYS cc_start: 0.7716 (mmpt) cc_final: 0.7443 (mmmt) REVERT: L 142 CYS cc_start: 0.6943 (t) cc_final: 0.5989 (t) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 1.6330 time to fit residues: 539.8072 Evaluate side-chains 242 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 135 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 177 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN G 53 GLN G 100 ASN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21377 Z= 0.261 Angle : 0.555 8.551 28878 Z= 0.299 Chirality : 0.044 0.164 3272 Planarity : 0.005 0.053 3698 Dihedral : 4.426 33.397 2913 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.23 % Allowed : 8.01 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 1.02 (0.16), residues: 2629 helix: 2.34 (0.17), residues: 962 sheet: 0.83 (0.21), residues: 549 loop : -0.93 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.023 0.001 PHE K 79 TYR 0.017 0.001 TYR B 136 ARG 0.010 0.000 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 258 time to evaluate : 2.599 Fit side-chains REVERT: A 215 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: B 230 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7161 (tt0) REVERT: C 102 VAL cc_start: 0.8674 (t) cc_final: 0.8434 (p) REVERT: F 100 ARG cc_start: 0.8233 (tpp80) cc_final: 0.8015 (ttm-80) REVERT: G 59 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: G 184 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7265 (mtmt) REVERT: H 80 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: J 96 LYS cc_start: 0.7709 (mmpt) cc_final: 0.7464 (mmpt) REVERT: K 26 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7471 (mt-10) REVERT: K 32 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5925 (ttm-80) REVERT: L 191 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7778 (mt-10) outliers start: 28 outliers final: 7 residues processed: 269 average time/residue: 1.5891 time to fit residues: 476.8801 Evaluate side-chains 254 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 241 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 177 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21377 Z= 0.213 Angle : 0.510 7.249 28878 Z= 0.275 Chirality : 0.043 0.155 3272 Planarity : 0.005 0.050 3698 Dihedral : 4.299 34.103 2913 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.72 % Allowed : 10.12 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 1.17 (0.16), residues: 2629 helix: 2.47 (0.17), residues: 962 sheet: 0.97 (0.21), residues: 552 loop : -0.89 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.021 0.001 PHE K 79 TYR 0.014 0.001 TYR F 239 ARG 0.007 0.000 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 252 time to evaluate : 2.507 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: B 230 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7113 (tt0) REVERT: C 102 VAL cc_start: 0.8625 (t) cc_final: 0.8380 (p) REVERT: D 191 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.6060 (tt) REVERT: F 72 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6678 (ptm160) REVERT: F 100 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7949 (ttm-80) REVERT: F 233 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7503 (mtp85) REVERT: G 184 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7070 (mtmt) REVERT: H 129 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.5845 (tm-30) REVERT: J 96 LYS cc_start: 0.7679 (mmpt) cc_final: 0.7426 (mmpt) REVERT: K 26 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7392 (mt-10) REVERT: L 155 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: L 191 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7884 (mt-10) outliers start: 39 outliers final: 14 residues processed: 269 average time/residue: 1.5965 time to fit residues: 479.0039 Evaluate side-chains 264 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.6980 chunk 181 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21377 Z= 0.230 Angle : 0.517 7.667 28878 Z= 0.277 Chirality : 0.043 0.158 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.300 34.114 2913 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.16 % Allowed : 11.17 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 1.16 (0.16), residues: 2629 helix: 2.44 (0.17), residues: 971 sheet: 0.93 (0.21), residues: 561 loop : -0.89 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.022 0.001 PHE K 79 TYR 0.015 0.001 TYR F 239 ARG 0.006 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 248 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: B 230 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7118 (tt0) REVERT: C 102 VAL cc_start: 0.8613 (t) cc_final: 0.8379 (p) REVERT: D 114 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6754 (tm-30) REVERT: D 191 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5946 (tt) REVERT: F 72 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6723 (ptm160) REVERT: F 100 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7972 (ttm-80) REVERT: G 184 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7119 (mtmt) REVERT: H 129 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: J 96 LYS cc_start: 0.7665 (mmpt) cc_final: 0.7433 (mmpt) REVERT: K 26 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7332 (mt-10) REVERT: L 191 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7869 (mt-10) outliers start: 49 outliers final: 16 residues processed: 269 average time/residue: 1.6153 time to fit residues: 484.6074 Evaluate side-chains 263 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.0980 chunk 145 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1152 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: