Starting phenix.real_space_refine on Mon Mar 18 13:20:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/03_2024/8qyl_18757_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/03_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_18757/03_2024/8qyl_18757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/03_2024/8qyl_18757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/03_2024/8qyl_18757_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyl_18757/03_2024/8qyl_18757_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20997 Number of models: 1 Model: "" Number of chains: 12 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: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1701 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 17 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: 10.77, per 1000 atoms: 0.51 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: 7.71 Conformation dependent library (CDL) restraints added in 3.8 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... running ksdssp... Secondary structure from input PDB file: 82 helices and 20 sheets defined 36.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.669A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 184 through 198 removed outlier: 4.669A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.604A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.738A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 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 168 through 178 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.789A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.553A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.943A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.719A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 240 Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.795A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) 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 86 through 103 Processing helix chain 'D' and resid 109 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 175 through 184 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'E' and resid 20 through 27 removed outlier: 3.668A pdb=" N GLU E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 105 through 120 removed outlier: 3.971A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.614A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.845A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU F 32 " --> pdb=" O MET F 28 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 Processing helix chain 'F' and resid 109 through 124 removed outlier: 3.555A pdb=" N TYR F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 removed outlier: 4.259A pdb=" N LYS F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 201 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 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'G' and resid 23 through 34 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) removed outlier: 4.272A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 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 172 through 185 Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.678A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 243 Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 55 through 70 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.684A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 114 through 117 No H-bonds generated for 'chain 'H' and resid 114 through 117' Processing helix chain 'H' and resid 130 through 137 Processing helix chain 'I' and resid 32 through 44 Processing helix chain 'I' and resid 62 through 65 No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'I' and resid 143 through 153 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 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 244 through 255 removed outlier: 4.042A pdb=" N PHE I 250 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 252 - end of helix removed outlier: 4.621A pdb=" N SER I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.160A pdb=" N VAL J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY J 28 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 39 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 69 No H-bonds generated for 'chain 'J' and resid 67 through 69' Processing helix chain 'J' and resid 99 through 113 Processing helix chain 'J' and resid 126 through 128 No H-bonds generated for 'chain 'J' and resid 126 through 128' Processing helix chain 'J' and resid 131 through 135 removed outlier: 3.599A pdb=" N ARG J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 131 through 135' Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 187 through 196 Processing helix chain 'J' and resid 214 through 228 removed outlier: 4.028A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 Processing helix chain 'K' and resid 92 through 113 Processing helix chain 'K' and resid 119 through 133 removed outlier: 3.741A pdb=" N TYR K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 183 removed outlier: 3.764A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 206 removed outlier: 3.585A pdb=" N GLY K 205 " --> pdb=" O ALA K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'L' and resid 57 through 78 removed outlier: 3.650A pdb=" N GLN L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 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 146 through 153 Processing helix chain 'L' and resid 160 through 172 Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 155 through 157 removed outlier: 3.518A pdb=" N CYS A 137 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 72 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 69 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 74 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing sheet with id= C, 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) Processing sheet with id= D, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.731A pdb=" N MET B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 69 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS B 74 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS B 67 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL B 76 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 158 through 161 Processing sheet with id= F, first strand: chain 'C' and resid 153 through 155 removed outlier: 3.524A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 69 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET C 71 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA C 64 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 62 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing sheet with id= G, 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= H, 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) Processing sheet with id= I, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= J, 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= K, first strand: chain 'F' and resid 163 through 166 Processing sheet with id= L, first strand: chain 'F' and resid 67 through 69 Processing sheet with id= M, 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= N, first strand: chain 'G' and resid 69 through 71 Processing sheet with id= O, 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: 6.297A pdb=" N GLN I 163 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE I 73 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR I 165 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE I 75 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU I 167 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 2 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: 6.601A pdb=" N ARG J 117 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET J 19 " --> pdb=" O ARG J 117 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE J 119 " --> pdb=" O MET J 19 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 140 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing sheet with id= Q, 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= R, first strand: chain 'K' and resid 162 through 164 removed outlier: 6.427A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY K 88 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE K 77 " --> pdb=" O GLY K 88 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 136 through 138 removed outlier: 3.500A pdb=" N VAL L 185 " --> pdb=" O LEU L 200 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 42 through 44 916 hydrogen bonds defined for protein. 2643 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: 6.00 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: 3059 2.76 - 3.30: 18368 3.30 - 3.83: 32416 3.83 - 4.37: 38791 4.37 - 4.90: 70269 Nonbonded interactions: 162903 Sorted by model distance: nonbonded pdb=" NH1 ARG A 143 " pdb=" O PRO A 144 " model vdw 2.225 2.520 nonbonded pdb=" NH1 ARG A 84 " pdb=" OD1 ASP G 120 " model vdw 2.247 2.520 nonbonded pdb=" OD2 ASP F 203 " pdb=" NZ LYS F 206 " model vdw 2.257 2.520 nonbonded pdb=" OG1 THR G 67 " pdb=" OE2 GLU G 216 " model vdw 2.265 2.440 nonbonded pdb=" O UNK K 249 " pdb=" NE2 GLN L 169 " model vdw 2.269 2.520 ... (remaining 162898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.530 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 53.580 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.540 ------------------------------------------------------------------------------- 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= 0.222 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 : 2.418 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: 1.6032 time to fit residues: 529.4228 Evaluate side-chains 242 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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: 2.9990 chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 E 68 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 100 ASN G 147 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 169 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21377 Z= 0.217 Angle : 0.514 8.154 28878 Z= 0.276 Chirality : 0.043 0.154 3272 Planarity : 0.005 0.049 3698 Dihedral : 4.300 33.268 2913 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.19 % Allowed : 8.10 % Favored : 90.72 % 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: 0.99 (0.16), residues: 2629 helix: 2.25 (0.17), residues: 956 sheet: 0.90 (0.21), residues: 541 loop : -0.90 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.019 0.001 PHE L 69 TYR 0.015 0.001 TYR B 136 ARG 0.011 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 281 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 2.343 Fit side-chains REVERT: A 215 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: B 230 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7244 (tt0) REVERT: D 107 MET cc_start: 0.7326 (ttm) cc_final: 0.7052 (mtm) REVERT: H 80 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: K 26 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7497 (mt-10) REVERT: K 107 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: L 171 MET cc_start: 0.7669 (tpt) cc_final: 0.7206 (tpt) REVERT: L 191 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7834 (mt-10) outliers start: 27 outliers final: 11 residues processed: 263 average time/residue: 1.5420 time to fit residues: 451.3969 Evaluate side-chains 256 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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 D residue 205 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 168 SER 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: 10.0000 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 239 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN G 147 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 103 ASN I 161 ASN I 224 GLN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 169 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21377 Z= 0.275 Angle : 0.535 7.659 28878 Z= 0.285 Chirality : 0.044 0.164 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.382 35.679 2913 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.80 % Allowed : 10.12 % Favored : 88.08 % 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: 0.98 (0.16), residues: 2629 helix: 2.20 (0.17), residues: 952 sheet: 0.97 (0.21), residues: 546 loop : -0.91 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.021 0.001 PHE L 69 TYR 0.017 0.001 TYR B 136 ARG 0.008 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 287 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 246 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: B 230 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7321 (tt0) REVERT: D 107 MET cc_start: 0.7346 (ttm) cc_final: 0.7059 (mtm) REVERT: D 114 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6696 (tm-30) REVERT: E 51 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6616 (mpt-90) REVERT: F 72 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6721 (ptm160) REVERT: G 184 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6913 (mtmm) REVERT: K 26 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7446 (mt-10) REVERT: L 191 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7853 (mt-10) outliers start: 41 outliers final: 18 residues processed: 264 average time/residue: 1.5093 time to fit residues: 444.3958 Evaluate side-chains 269 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 139 ASP 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 46 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain K residue 96 ASP 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: 3.9990 chunk 181 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 103 ASN I 161 ASN I 224 GLN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN L 169 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0985 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= 0.192 Angle : 0.488 7.181 28878 Z= 0.261 Chirality : 0.042 0.148 3272 Planarity : 0.005 0.049 3698 Dihedral : 4.240 34.568 2913 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.07 % Allowed : 11.35 % Favored : 86.58 % 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: 1.10 (0.16), residues: 2629 helix: 2.30 (0.17), residues: 950 sheet: 1.09 (0.21), residues: 542 loop : -0.86 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 216 HIS 0.004 0.001 HIS I 125 PHE 0.019 0.001 PHE L 69 TYR 0.015 0.001 TYR F 239 ARG 0.005 0.000 ARG I 51 *********************** 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 294 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 2.491 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: B 230 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7315 (tt0) REVERT: D 107 MET cc_start: 0.7330 (ttm) cc_final: 0.7006 (mtm) REVERT: D 114 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6582 (tm-30) REVERT: E 51 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6720 (mpt-90) REVERT: F 72 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6724 (ptm160) REVERT: G 59 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: H 62 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6813 (ptt) REVERT: H 129 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6113 (tm-30) REVERT: I 280 ASN cc_start: 0.6354 (OUTLIER) cc_final: 0.6029 (m-40) REVERT: K 26 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7377 (mt-10) REVERT: K 107 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: L 155 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: L 191 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7854 (mt-10) outliers start: 47 outliers final: 14 residues processed: 269 average time/residue: 1.5833 time to fit residues: 474.0401 Evaluate side-chains 271 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 E residue 51 ARG Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 155 GLU 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: 8.9990 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 230 optimal weight: 0.0980 chunk 64 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 103 ASN I 161 ASN I 224 GLN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21377 Z= 0.268 Angle : 0.528 8.115 28878 Z= 0.280 Chirality : 0.043 0.163 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.352 36.027 2913 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.29 % Allowed : 11.79 % Favored : 85.92 % 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: 1.01 (0.16), residues: 2629 helix: 2.21 (0.17), residues: 952 sheet: 1.00 (0.21), residues: 552 loop : -0.90 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 216 HIS 0.004 0.001 HIS I 125 PHE 0.021 0.001 PHE L 69 TYR 0.017 0.001 TYR F 239 ARG 0.007 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 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 303 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 251 time to evaluate : 2.689 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: B 230 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7338 (tt0) REVERT: D 114 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6568 (tm-30) REVERT: E 51 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6898 (mpt-90) REVERT: F 72 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6730 (ptm160) REVERT: G 59 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7974 (ttpt) REVERT: H 129 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: I 88 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8166 (mmm) REVERT: I 280 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.6147 (m-40) REVERT: I 281 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6111 (pp20) REVERT: K 26 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7494 (mt-10) REVERT: K 107 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: L 149 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7204 (mtp) REVERT: L 191 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7905 (mt-10) outliers start: 52 outliers final: 21 residues processed: 277 average time/residue: 1.6018 time to fit residues: 495.4484 Evaluate side-chains 277 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 C residue 104 VAL 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 E residue 51 ARG 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 190 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 149 MET Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 103 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN L 169 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21377 Z= 0.226 Angle : 0.509 8.198 28878 Z= 0.270 Chirality : 0.043 0.156 3272 Planarity : 0.005 0.050 3698 Dihedral : 4.285 36.025 2913 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 12.89 % Favored : 85.17 % 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: 1.04 (0.16), residues: 2629 helix: 2.24 (0.17), residues: 952 sheet: 1.02 (0.21), residues: 552 loop : -0.88 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 100 HIS 0.004 0.001 HIS D 73 PHE 0.020 0.001 PHE L 69 TYR 0.016 0.001 TYR F 239 ARG 0.008 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 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 292 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 248 time to evaluate : 2.275 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: B 230 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7333 (tt0) REVERT: D 107 MET cc_start: 0.7297 (ttm) cc_final: 0.6962 (mtm) REVERT: D 114 GLN cc_start: 0.6993 (tm-30) cc_final: 0.6580 (tm-30) REVERT: D 210 LEU cc_start: 0.7723 (mp) cc_final: 0.6999 (mt) REVERT: E 51 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6879 (mpt-90) REVERT: F 72 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6715 (ptm160) REVERT: G 59 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7990 (ttpt) REVERT: H 129 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6217 (tm-30) REVERT: I 88 MET cc_start: 0.8418 (mtm) cc_final: 0.8179 (mmm) REVERT: I 280 ASN cc_start: 0.6394 (OUTLIER) cc_final: 0.6119 (m-40) REVERT: K 107 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: L 183 MET cc_start: 0.7620 (ptt) cc_final: 0.7287 (pmm) REVERT: L 191 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7941 (mt-10) outliers start: 44 outliers final: 20 residues processed: 270 average time/residue: 1.5343 time to fit residues: 461.3691 Evaluate side-chains 276 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 248 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP 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 C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU 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 E residue 51 ARG 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 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 103 ASN I 161 ASN I 163 GLN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21377 Z= 0.366 Angle : 0.585 9.191 28878 Z= 0.309 Chirality : 0.046 0.177 3272 Planarity : 0.005 0.053 3698 Dihedral : 4.548 38.991 2913 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.42 % Allowed : 13.37 % Favored : 84.21 % 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: 0.85 (0.16), residues: 2629 helix: 2.06 (0.17), residues: 951 sheet: 0.98 (0.21), residues: 546 loop : -0.98 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.023 0.002 PHE L 69 TYR 0.019 0.002 TYR B 136 ARG 0.009 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 7 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 309 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: B 230 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7388 (tt0) REVERT: D 107 MET cc_start: 0.7339 (ttm) cc_final: 0.7006 (mtm) REVERT: D 114 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6600 (tm-30) REVERT: D 210 LEU cc_start: 0.7732 (mp) cc_final: 0.7040 (mt) REVERT: E 51 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7065 (mpt-90) REVERT: F 72 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6780 (ptm160) REVERT: G 59 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8005 (ttpt) REVERT: H 129 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6275 (tm-30) REVERT: I 88 MET cc_start: 0.8428 (mtm) cc_final: 0.8198 (mmm) REVERT: I 101 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8303 (pp) REVERT: I 280 ASN cc_start: 0.6400 (OUTLIER) cc_final: 0.6133 (m-40) REVERT: K 26 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7538 (mt-10) REVERT: K 107 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: L 183 MET cc_start: 0.7657 (ptt) cc_final: 0.7318 (pmm) REVERT: L 191 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7928 (mt-10) outliers start: 55 outliers final: 27 residues processed: 283 average time/residue: 1.5107 time to fit residues: 477.3666 Evaluate side-chains 281 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU 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 E residue 51 ARG 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 190 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1184 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= 0.181 Angle : 0.486 7.121 28878 Z= 0.259 Chirality : 0.042 0.143 3272 Planarity : 0.005 0.049 3698 Dihedral : 4.243 37.530 2913 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.98 % Allowed : 14.12 % Favored : 83.90 % 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: 1.05 (0.16), residues: 2629 helix: 2.25 (0.17), residues: 950 sheet: 1.03 (0.21), residues: 552 loop : -0.87 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.018 0.001 PHE L 69 TYR 0.016 0.001 TYR F 239 ARG 0.012 0.000 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 8 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 292 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 2.407 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: B 230 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7360 (tt0) REVERT: D 107 MET cc_start: 0.7274 (ttm) cc_final: 0.6939 (mtm) REVERT: D 114 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6583 (tm-30) REVERT: D 210 LEU cc_start: 0.7708 (mp) cc_final: 0.6989 (mt) REVERT: E 51 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7047 (mpt-90) REVERT: F 72 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6704 (ptm160) REVERT: G 59 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7987 (ttpt) REVERT: H 129 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: I 88 MET cc_start: 0.8430 (mtm) cc_final: 0.8210 (mmm) REVERT: I 101 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8271 (pp) REVERT: I 280 ASN cc_start: 0.6331 (OUTLIER) cc_final: 0.6087 (m-40) REVERT: I 281 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6188 (pp20) REVERT: K 26 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7584 (mt-10) REVERT: K 107 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: L 183 MET cc_start: 0.7655 (ptt) cc_final: 0.7406 (pmm) REVERT: L 191 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7936 (mt-10) outliers start: 45 outliers final: 22 residues processed: 272 average time/residue: 1.5423 time to fit residues: 467.5900 Evaluate side-chains 274 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 198 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21377 Z= 0.366 Angle : 0.586 9.287 28878 Z= 0.309 Chirality : 0.045 0.176 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.533 40.542 2913 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.16 % Allowed : 14.30 % Favored : 83.55 % 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: 0.84 (0.16), residues: 2629 helix: 2.03 (0.17), residues: 951 sheet: 0.98 (0.21), residues: 550 loop : -0.99 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 102 HIS 0.005 0.001 HIS I 125 PHE 0.023 0.002 PHE L 69 TYR 0.019 0.002 TYR F 239 ARG 0.011 0.000 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 9 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 299 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 250 time to evaluate : 2.434 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: B 230 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7402 (tt0) REVERT: D 107 MET cc_start: 0.7338 (ttm) cc_final: 0.7043 (mtm) REVERT: D 114 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6608 (tm-30) REVERT: D 210 LEU cc_start: 0.7723 (mp) cc_final: 0.6978 (mt) REVERT: D 226 PHE cc_start: 0.3800 (OUTLIER) cc_final: 0.1947 (m-10) REVERT: E 51 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7207 (mpt-90) REVERT: F 72 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6789 (ptm160) REVERT: G 59 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (ttpt) REVERT: H 129 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: I 88 MET cc_start: 0.8435 (mtm) cc_final: 0.8219 (mmm) REVERT: I 101 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8315 (pp) REVERT: I 280 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6138 (m-40) REVERT: I 281 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6214 (pp20) REVERT: K 26 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7552 (mt-10) REVERT: K 107 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: L 183 MET cc_start: 0.7712 (ptt) cc_final: 0.7370 (pmm) REVERT: L 191 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7996 (mt-10) outliers start: 49 outliers final: 25 residues processed: 280 average time/residue: 1.5191 time to fit residues: 474.5424 Evaluate side-chains 281 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU 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 226 PHE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN D 214 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 161 ASN J 153 ASN J 159 ASN L 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21377 Z= 0.157 Angle : 0.479 8.329 28878 Z= 0.255 Chirality : 0.041 0.143 3272 Planarity : 0.005 0.047 3698 Dihedral : 4.194 38.394 2913 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.80 % Allowed : 14.74 % Favored : 83.46 % 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: 1.08 (0.16), residues: 2629 helix: 2.27 (0.17), residues: 950 sheet: 1.07 (0.21), residues: 551 loop : -0.86 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.017 0.001 PHE L 69 TYR 0.017 0.001 TYR F 239 ARG 0.010 0.000 ARG F 188 ********************** REFINEMENT MACRO_CYCLE 10 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: 41 poor density : 245 time to evaluate : 2.399 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: B 230 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7358 (tt0) REVERT: D 107 MET cc_start: 0.7271 (ttm) cc_final: 0.7009 (mtm) REVERT: D 114 GLN cc_start: 0.7002 (tm-30) cc_final: 0.6548 (tm-30) REVERT: D 210 LEU cc_start: 0.7645 (mp) cc_final: 0.6926 (mt) REVERT: E 51 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7002 (mpt-90) REVERT: F 72 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6687 (ptm160) REVERT: G 59 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: H 129 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6221 (tm-30) REVERT: I 88 MET cc_start: 0.8422 (mtm) cc_final: 0.8211 (mmm) REVERT: I 101 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8226 (pp) REVERT: I 103 ASN cc_start: 0.7389 (m110) cc_final: 0.7102 (m-40) REVERT: I 162 MET cc_start: 0.7419 (ttm) cc_final: 0.7218 (ttp) REVERT: I 280 ASN cc_start: 0.6122 (OUTLIER) cc_final: 0.5883 (m-40) REVERT: I 281 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6117 (pp20) REVERT: K 26 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7557 (mt-10) REVERT: K 107 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: L 191 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7920 (mt-10) outliers start: 41 outliers final: 23 residues processed: 270 average time/residue: 1.4667 time to fit residues: 441.6383 Evaluate side-chains 275 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 242 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 51 ARG 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 46 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 204 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** G 53 GLN G 147 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 161 ASN J 153 ASN L 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.077772 restraints weight = 30666.394| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.42 r_work: 0.2806 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 21377 Z= 0.438 Angle : 0.629 9.924 28878 Z= 0.331 Chirality : 0.047 0.185 3272 Planarity : 0.006 0.056 3698 Dihedral : 4.638 41.360 2913 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 14.65 % Favored : 83.24 % 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: 0.78 (0.16), residues: 2629 helix: 1.97 (0.17), residues: 951 sheet: 0.94 (0.21), residues: 552 loop : -1.02 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 102 HIS 0.006 0.001 HIS I 125 PHE 0.024 0.002 PHE L 69 TYR 0.021 0.002 TYR B 136 ARG 0.014 0.001 ARG F 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7960.79 seconds wall clock time: 141 minutes 20.29 seconds (8480.29 seconds total)