Starting phenix.real_space_refine on Tue Feb 13 13:39:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/02_2024/8dwh_27754_updated.pdb" } resolution = 3.25 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= 0.001 sd= 0.023 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 44 5.16 5 C 4136 2.51 5 N 1103 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6444 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1910 Unusual residues: {'U2U': 1} Classifications: {'peptide': 248, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 241, None: 1} Not linked: pdbres="PHE R 278 " pdbres="U2U R 401 " Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 3.98, per 1000 atoms: 0.62 Number of scatterers: 6444 At special positions: 0 Unit cell: (90.64, 101.2, 121.44, 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 44 16.00 O 1161 8.00 N 1103 7.00 C 4136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 9 sheets defined 41.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.603A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.756A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.710A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 242 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'R' and resid 26 through 54 removed outlier: 4.027A pdb=" N GLY R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS R 54 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 87 removed outlier: 3.829A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE R 87 " --> pdb=" O SER R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 125 removed outlier: 4.397A pdb=" N LEU R 98 " --> pdb=" O SER R 95 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR R 99 " --> pdb=" O LYS R 96 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 5.558A pdb=" N MET R 103 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE R 107 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 108 " --> pdb=" O SER R 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU R 110 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER R 114 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 116 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'R' and resid 136 through 160 removed outlier: 4.446A pdb=" N SER R 139 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 140 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL R 142 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS R 143 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU R 146 " --> pdb=" O CYS R 143 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG R 153 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE R 155 " --> pdb=" O LEU R 152 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET R 159 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU R 160 " --> pdb=" O GLU R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 203 Processing helix chain 'R' and resid 212 through 228 removed outlier: 3.873A pdb=" N PHE R 225 " --> pdb=" O THR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 234 No H-bonds generated for 'chain 'R' and resid 231 through 234' Processing helix chain 'R' and resid 238 through 241 No H-bonds generated for 'chain 'R' and resid 238 through 241' Processing helix chain 'R' and resid 246 through 251 removed outlier: 4.125A pdb=" N PHE R 250 " --> pdb=" O ARG R 246 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 246 through 251' Processing helix chain 'R' and resid 255 through 272 removed outlier: 3.524A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) Proline residue: R 269 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.829A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 38 through 40 removed outlier: 8.178A pdb=" N LEU B 39 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 107 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 138 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE B 108 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE B 140 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL B 110 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 142 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.861A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.675A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.662A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.718A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.525A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.628A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 759 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: 2.03 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2079 1.34 - 1.46: 1452 1.46 - 1.58: 2990 1.58 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 6578 Sorted by residual: bond pdb=" C22 U2U R 401 " pdb=" N3 U2U R 401 " ideal model delta sigma weight residual 1.453 1.341 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" N1 U2U R 401 " pdb=" S1 U2U R 401 " ideal model delta sigma weight residual 1.713 1.628 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C17 U2U R 401 " pdb=" C18 U2U R 401 " ideal model delta sigma weight residual 1.351 1.414 -0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" C7 U2U R 401 " pdb=" S1 U2U R 401 " ideal model delta sigma weight residual 1.817 1.760 0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C2 U2U R 401 " pdb=" O1 U2U R 401 " ideal model delta sigma weight residual 1.403 1.358 0.045 2.00e-02 2.50e+03 5.15e+00 ... (remaining 6573 not shown) Histogram of bond angle deviations from ideal: 100.61 - 107.30: 169 107.30 - 114.00: 3760 114.00 - 120.69: 2781 120.69 - 127.38: 2186 127.38 - 134.08: 68 Bond angle restraints: 8964 Sorted by residual: angle pdb=" C17 U2U R 401 " pdb=" C22 U2U R 401 " pdb=" N3 U2U R 401 " ideal model delta sigma weight residual 147.58 121.24 26.34 3.00e+00 1.11e-01 7.71e+01 angle pdb=" N2 U2U R 401 " pdb=" C22 U2U R 401 " pdb=" N3 U2U R 401 " ideal model delta sigma weight residual 92.15 117.90 -25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" C19 U2U R 401 " pdb=" C14 U2U R 401 " pdb=" O4 U2U R 401 " ideal model delta sigma weight residual 140.79 120.36 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" C12 U2U R 401 " pdb=" C13 U2U R 401 " pdb=" O4 U2U R 401 " ideal model delta sigma weight residual 101.58 120.28 -18.70 3.00e+00 1.11e-01 3.88e+01 angle pdb=" C15 U2U R 401 " pdb=" C14 U2U R 401 " pdb=" O4 U2U R 401 " ideal model delta sigma weight residual 99.20 117.63 -18.43 3.00e+00 1.11e-01 3.78e+01 ... (remaining 8959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3493 17.84 - 35.68: 278 35.68 - 53.52: 49 53.52 - 71.36: 4 71.36 - 89.19: 1 Dihedral angle restraints: 3825 sinusoidal: 1330 harmonic: 2495 Sorted by residual: dihedral pdb=" C7 U2U R 401 " pdb=" N1 U2U R 401 " pdb=" S1 U2U R 401 " pdb=" C8 U2U R 401 " ideal model delta sinusoidal sigma weight residual 200.27 111.08 89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA PRO R 100 " pdb=" C PRO R 100 " pdb=" N VAL R 101 " pdb=" CA VAL R 101 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASN B 223 " pdb=" CB ASN B 223 " pdb=" CG ASN B 223 " pdb=" OD1 ASN B 223 " ideal model delta sinusoidal sigma weight residual 120.00 -175.31 -64.69 2 2.00e+01 2.50e-03 9.81e+00 ... (remaining 3822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 619 0.030 - 0.060: 296 0.060 - 0.090: 90 0.090 - 0.120: 46 0.120 - 0.150: 10 Chirality restraints: 1061 Sorted by residual: chirality pdb=" CA PRO R 231 " pdb=" N PRO R 231 " pdb=" C PRO R 231 " pdb=" CB PRO R 231 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CG LEU R 191 " pdb=" CB LEU R 191 " pdb=" CD1 LEU R 191 " pdb=" CD2 LEU R 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ASN B 43 " pdb=" N ASN B 43 " pdb=" C ASN B 43 " pdb=" CB ASN B 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1058 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 230 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO R 231 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO C 236 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO D 49 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.020 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 117 2.68 - 3.24: 6341 3.24 - 3.79: 9809 3.79 - 4.35: 13375 4.35 - 4.90: 22176 Nonbonded interactions: 51818 Sorted by model distance: nonbonded pdb=" OH TYR R 64 " pdb=" OE2 GLU R 119 " model vdw 2.129 2.440 nonbonded pdb=" OD1 ASP C 153 " pdb=" N ASP C 154 " model vdw 2.133 2.520 nonbonded pdb=" OH TYR B 243 " pdb=" OH TYR R 130 " model vdw 2.159 2.440 nonbonded pdb=" OE1 GLU B 182 " pdb=" OG1 THR B 187 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR R 106 " pdb=" O PHE R 232 " model vdw 2.216 2.440 ... (remaining 51813 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.910 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.800 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 6578 Z= 0.304 Angle : 0.848 26.345 8964 Z= 0.374 Chirality : 0.042 0.150 1061 Planarity : 0.003 0.052 1122 Dihedral : 13.054 89.195 2200 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 844 helix: 0.07 (0.28), residues: 356 sheet: -0.32 (0.45), residues: 145 loop : -1.41 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE C 199 TYR 0.009 0.001 TYR C 105 ARG 0.011 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.753 Fit side-chains REVERT: B 122 LEU cc_start: 0.7986 (mp) cc_final: 0.7733 (mp) REVERT: B 128 ILE cc_start: 0.8048 (mm) cc_final: 0.7847 (mt) REVERT: B 145 LYS cc_start: 0.8297 (mtpp) cc_final: 0.8001 (mtpt) REVERT: B 210 ILE cc_start: 0.8138 (mt) cc_final: 0.7906 (mt) REVERT: C 68 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7497 (ttt-90) REVERT: C 134 ARG cc_start: 0.6814 (pmt-80) cc_final: 0.6428 (pmt-80) REVERT: C 258 ASP cc_start: 0.7135 (t70) cc_final: 0.6340 (t0) REVERT: C 285 LEU cc_start: 0.8462 (tt) cc_final: 0.8258 (tt) REVERT: R 65 ILE cc_start: 0.7733 (mm) cc_final: 0.7487 (mt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2421 time to fit residues: 48.9845 Evaluate side-chains 145 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.3980 chunk 63 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6578 Z= 0.214 Angle : 0.555 9.283 8964 Z= 0.286 Chirality : 0.042 0.139 1061 Planarity : 0.004 0.035 1122 Dihedral : 5.214 96.660 917 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.24 % Allowed : 7.93 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 844 helix: 0.87 (0.28), residues: 360 sheet: -0.20 (0.41), residues: 163 loop : -1.35 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.010 0.001 PHE C 199 TYR 0.009 0.001 TYR R 64 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 0.771 Fit side-chains REVERT: B 8 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6325 (tm-30) REVERT: B 145 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7996 (mtpt) REVERT: B 192 PHE cc_start: 0.7588 (t80) cc_final: 0.7261 (t80) REVERT: B 194 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7405 (tmm-80) REVERT: C 68 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7483 (ttt90) REVERT: C 134 ARG cc_start: 0.6840 (pmt-80) cc_final: 0.6477 (pmt-80) REVERT: C 258 ASP cc_start: 0.7152 (t70) cc_final: 0.6255 (t0) REVERT: C 285 LEU cc_start: 0.8455 (tt) cc_final: 0.8225 (tt) REVERT: R 51 LEU cc_start: 0.8122 (mt) cc_final: 0.7779 (mp) REVERT: R 73 PHE cc_start: 0.8134 (t80) cc_final: 0.7897 (t80) REVERT: R 158 TRP cc_start: 0.7413 (t60) cc_final: 0.7177 (t60) outliers start: 8 outliers final: 6 residues processed: 163 average time/residue: 0.2623 time to fit residues: 53.0364 Evaluate side-chains 157 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6578 Z= 0.252 Angle : 0.556 8.607 8964 Z= 0.280 Chirality : 0.042 0.134 1061 Planarity : 0.004 0.037 1122 Dihedral : 5.202 98.487 917 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.80 % Allowed : 10.42 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 844 helix: 1.22 (0.29), residues: 357 sheet: -0.18 (0.39), residues: 175 loop : -1.36 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.011 0.001 PHE R 178 TYR 0.013 0.001 TYR C 59 ARG 0.009 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6356 (tm-30) REVERT: B 32 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: B 33 THR cc_start: 0.8523 (t) cc_final: 0.8209 (p) REVERT: B 145 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8009 (mtpt) REVERT: C 68 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7421 (ttt90) REVERT: C 134 ARG cc_start: 0.6832 (pmt-80) cc_final: 0.6494 (pmt-80) REVERT: C 258 ASP cc_start: 0.7183 (t70) cc_final: 0.6238 (t0) REVERT: C 285 LEU cc_start: 0.8432 (tt) cc_final: 0.8159 (tt) REVERT: R 51 LEU cc_start: 0.8106 (mt) cc_final: 0.7785 (mp) REVERT: R 73 PHE cc_start: 0.8156 (t80) cc_final: 0.7872 (t80) REVERT: R 158 TRP cc_start: 0.7432 (t60) cc_final: 0.7215 (t60) outliers start: 18 outliers final: 10 residues processed: 162 average time/residue: 0.2464 time to fit residues: 49.3307 Evaluate side-chains 163 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6578 Z= 0.266 Angle : 0.540 8.082 8964 Z= 0.276 Chirality : 0.042 0.136 1061 Planarity : 0.004 0.032 1122 Dihedral : 5.230 99.499 917 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.58 % Allowed : 12.60 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.30), residues: 844 helix: 1.36 (0.29), residues: 357 sheet: -0.13 (0.39), residues: 175 loop : -1.32 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.001 PHE C 278 TYR 0.012 0.001 TYR C 59 ARG 0.007 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6392 (tm-30) REVERT: B 32 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7130 (mtm-85) REVERT: B 33 THR cc_start: 0.8529 (t) cc_final: 0.8248 (p) REVERT: B 73 LYS cc_start: 0.7554 (mttm) cc_final: 0.7175 (mttm) REVERT: C 61 MET cc_start: 0.6858 (ppp) cc_final: 0.6296 (ppp) REVERT: C 68 ARG cc_start: 0.8074 (ttt180) cc_final: 0.7351 (ttt90) REVERT: C 134 ARG cc_start: 0.6824 (pmt-80) cc_final: 0.6419 (pmt-80) REVERT: C 188 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6767 (mtp) REVERT: C 219 ARG cc_start: 0.6857 (mtt180) cc_final: 0.6611 (mtt90) REVERT: C 258 ASP cc_start: 0.7190 (t70) cc_final: 0.6221 (t0) REVERT: C 285 LEU cc_start: 0.8401 (tt) cc_final: 0.8120 (tt) REVERT: R 34 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.7010 (t) REVERT: R 51 LEU cc_start: 0.8100 (mt) cc_final: 0.7769 (mp) REVERT: R 73 PHE cc_start: 0.8134 (t80) cc_final: 0.7820 (t80) REVERT: R 158 TRP cc_start: 0.7447 (t60) cc_final: 0.7239 (t60) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.2816 time to fit residues: 54.1154 Evaluate side-chains 166 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6578 Z= 0.266 Angle : 0.538 7.943 8964 Z= 0.275 Chirality : 0.042 0.154 1061 Planarity : 0.004 0.032 1122 Dihedral : 5.234 100.052 917 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.35 % Allowed : 13.37 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.30), residues: 844 helix: 1.40 (0.29), residues: 359 sheet: -0.11 (0.40), residues: 165 loop : -1.32 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE C 278 TYR 0.011 0.001 TYR C 59 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6394 (tm-30) REVERT: B 32 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.7146 (mtm-85) REVERT: B 33 THR cc_start: 0.8492 (t) cc_final: 0.8280 (p) REVERT: B 73 LYS cc_start: 0.7525 (mttm) cc_final: 0.7128 (mttm) REVERT: B 145 LYS cc_start: 0.8257 (mtpp) cc_final: 0.8014 (mtpt) REVERT: C 61 MET cc_start: 0.6806 (ppp) cc_final: 0.6316 (ppp) REVERT: C 68 ARG cc_start: 0.8064 (ttt180) cc_final: 0.7315 (ttt90) REVERT: C 134 ARG cc_start: 0.6829 (pmt-80) cc_final: 0.6389 (pmt-80) REVERT: C 188 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6787 (mtp) REVERT: C 258 ASP cc_start: 0.7194 (t70) cc_final: 0.6222 (t0) REVERT: C 285 LEU cc_start: 0.8358 (tt) cc_final: 0.8099 (tt) REVERT: R 34 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.7002 (t) REVERT: R 51 LEU cc_start: 0.8083 (mt) cc_final: 0.7747 (mp) REVERT: R 73 PHE cc_start: 0.8164 (t80) cc_final: 0.7849 (t80) outliers start: 28 outliers final: 19 residues processed: 158 average time/residue: 0.2811 time to fit residues: 54.1590 Evaluate side-chains 166 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 67 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6578 Z= 0.161 Angle : 0.493 7.303 8964 Z= 0.253 Chirality : 0.040 0.135 1061 Planarity : 0.004 0.042 1122 Dihedral : 5.106 100.765 917 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.95 % Allowed : 15.24 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 844 helix: 1.59 (0.29), residues: 359 sheet: -0.17 (0.40), residues: 165 loop : -1.28 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 158 HIS 0.011 0.001 HIS B 82 PHE 0.011 0.001 PHE R 178 TYR 0.010 0.001 TYR C 59 ARG 0.010 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 0.656 Fit side-chains REVERT: B 8 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6324 (tm-30) REVERT: B 32 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.7188 (mtm-85) REVERT: B 33 THR cc_start: 0.8468 (t) cc_final: 0.8239 (p) REVERT: B 194 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7406 (tmm-80) REVERT: C 61 MET cc_start: 0.6586 (ppp) cc_final: 0.6154 (ppp) REVERT: C 68 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7379 (ttt-90) REVERT: C 134 ARG cc_start: 0.6827 (pmt-80) cc_final: 0.6482 (pmt-80) REVERT: C 188 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6688 (mtp) REVERT: C 258 ASP cc_start: 0.7176 (t70) cc_final: 0.6230 (t0) REVERT: C 283 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7750 (tpt-90) REVERT: C 285 LEU cc_start: 0.8301 (tt) cc_final: 0.8030 (tt) REVERT: R 73 PHE cc_start: 0.8168 (t80) cc_final: 0.7769 (t80) outliers start: 19 outliers final: 13 residues processed: 159 average time/residue: 0.2861 time to fit residues: 57.0636 Evaluate side-chains 164 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.0370 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6578 Z= 0.159 Angle : 0.476 6.724 8964 Z= 0.245 Chirality : 0.040 0.127 1061 Planarity : 0.003 0.042 1122 Dihedral : 5.020 100.925 917 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.27 % Allowed : 16.64 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 844 helix: 1.85 (0.29), residues: 351 sheet: -0.24 (0.40), residues: 165 loop : -1.22 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 158 HIS 0.003 0.001 HIS B 209 PHE 0.010 0.001 PHE R 178 TYR 0.008 0.001 TYR C 59 ARG 0.010 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6277 (tm-30) REVERT: B 32 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: B 33 THR cc_start: 0.8488 (t) cc_final: 0.8243 (p) REVERT: B 145 LYS cc_start: 0.8316 (mtpp) cc_final: 0.8021 (mtpt) REVERT: B 188 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7627 (ttp80) REVERT: B 194 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7410 (tmm-80) REVERT: C 61 MET cc_start: 0.6454 (ppp) cc_final: 0.6045 (ppp) REVERT: C 68 ARG cc_start: 0.8041 (ttt180) cc_final: 0.7394 (ttt-90) REVERT: C 134 ARG cc_start: 0.6843 (pmt-80) cc_final: 0.6508 (pmt-80) REVERT: C 188 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6694 (mtp) REVERT: C 195 ASP cc_start: 0.7346 (p0) cc_final: 0.7118 (p0) REVERT: C 258 ASP cc_start: 0.7209 (t70) cc_final: 0.6320 (t0) REVERT: C 283 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7751 (tpt-90) REVERT: C 285 LEU cc_start: 0.8268 (tt) cc_final: 0.8006 (tt) REVERT: C 338 ILE cc_start: 0.8340 (mm) cc_final: 0.7935 (mm) REVERT: R 73 PHE cc_start: 0.8130 (t80) cc_final: 0.7835 (t80) REVERT: R 76 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7325 (mm) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.2624 time to fit residues: 53.9006 Evaluate side-chains 169 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.0470 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 0.0070 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 73 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.0770 overall best weight: 0.1312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6578 Z= 0.123 Angle : 0.465 9.058 8964 Z= 0.236 Chirality : 0.039 0.132 1061 Planarity : 0.003 0.038 1122 Dihedral : 4.856 100.760 917 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 17.88 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 844 helix: 2.04 (0.29), residues: 354 sheet: -0.19 (0.38), residues: 171 loop : -1.17 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 158 HIS 0.003 0.001 HIS C 62 PHE 0.010 0.001 PHE R 178 TYR 0.008 0.001 TYR C 59 ARG 0.009 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.744 Fit side-chains REVERT: B 8 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6249 (tm-30) REVERT: B 32 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.7149 (mtm-85) REVERT: B 33 THR cc_start: 0.8514 (t) cc_final: 0.8185 (p) REVERT: B 73 LYS cc_start: 0.7677 (mttm) cc_final: 0.7459 (mttm) REVERT: B 145 LYS cc_start: 0.8289 (mtpp) cc_final: 0.8038 (mtpt) REVERT: B 194 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.7261 (ttm-80) REVERT: B 195 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7256 (ttpp) REVERT: C 68 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7515 (ttt90) REVERT: C 101 MET cc_start: 0.7636 (mtt) cc_final: 0.7340 (mtt) REVERT: C 134 ARG cc_start: 0.6840 (pmt-80) cc_final: 0.6570 (pmt-80) REVERT: C 195 ASP cc_start: 0.7320 (p0) cc_final: 0.7084 (p0) REVERT: C 258 ASP cc_start: 0.7221 (t70) cc_final: 0.6345 (t0) REVERT: C 285 LEU cc_start: 0.8099 (tt) cc_final: 0.7852 (tt) REVERT: R 51 LEU cc_start: 0.8053 (mt) cc_final: 0.7725 (mp) REVERT: R 73 PHE cc_start: 0.8154 (t80) cc_final: 0.7901 (t80) REVERT: R 76 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7283 (mm) outliers start: 18 outliers final: 14 residues processed: 165 average time/residue: 0.2606 time to fit residues: 54.8004 Evaluate side-chains 165 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 98 GLN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6578 Z= 0.179 Angle : 0.484 8.090 8964 Z= 0.246 Chirality : 0.041 0.146 1061 Planarity : 0.003 0.042 1122 Dihedral : 4.911 101.076 917 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.49 % Allowed : 19.13 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 844 helix: 2.02 (0.29), residues: 354 sheet: -0.09 (0.40), residues: 163 loop : -1.21 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 158 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.001 PHE R 178 TYR 0.008 0.001 TYR R 106 ARG 0.010 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.787 Fit side-chains REVERT: B 8 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6293 (tm-30) REVERT: B 32 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.7184 (mtm-85) REVERT: B 33 THR cc_start: 0.8513 (t) cc_final: 0.8197 (p) REVERT: B 73 LYS cc_start: 0.7691 (mttm) cc_final: 0.7468 (mttm) REVERT: B 145 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8048 (mtpt) REVERT: B 188 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7604 (ttp80) REVERT: B 194 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7258 (ttm-80) REVERT: C 68 ARG cc_start: 0.8024 (ttt180) cc_final: 0.7327 (ttt-90) REVERT: C 101 MET cc_start: 0.7732 (mtt) cc_final: 0.7383 (mtt) REVERT: C 134 ARG cc_start: 0.6837 (pmt-80) cc_final: 0.6540 (pmt-80) REVERT: C 195 ASP cc_start: 0.7343 (p0) cc_final: 0.7114 (p0) REVERT: C 258 ASP cc_start: 0.7211 (t70) cc_final: 0.6333 (t0) REVERT: C 285 LEU cc_start: 0.8118 (tt) cc_final: 0.7883 (tt) REVERT: R 51 LEU cc_start: 0.8030 (mt) cc_final: 0.7690 (mp) REVERT: R 73 PHE cc_start: 0.8112 (t80) cc_final: 0.7862 (t80) REVERT: R 76 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7284 (mm) outliers start: 16 outliers final: 13 residues processed: 161 average time/residue: 0.2921 time to fit residues: 59.4710 Evaluate side-chains 163 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6578 Z= 0.236 Angle : 0.520 8.229 8964 Z= 0.263 Chirality : 0.042 0.203 1061 Planarity : 0.004 0.043 1122 Dihedral : 5.086 101.719 917 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.33 % Allowed : 18.97 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.30), residues: 844 helix: 1.74 (0.29), residues: 364 sheet: -0.09 (0.40), residues: 163 loop : -1.26 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 158 HIS 0.004 0.001 HIS B 209 PHE 0.013 0.001 PHE R 178 TYR 0.010 0.001 TYR C 59 ARG 0.010 0.001 ARG B 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.764 Fit side-chains REVERT: B 8 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6343 (tm-30) REVERT: B 32 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7193 (mtm-85) REVERT: B 33 THR cc_start: 0.8452 (t) cc_final: 0.8235 (p) REVERT: B 73 LYS cc_start: 0.7682 (mttm) cc_final: 0.7473 (mttm) REVERT: B 145 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8025 (mtpt) REVERT: B 188 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7594 (ttp80) REVERT: B 194 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7376 (tmm-80) REVERT: C 68 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7264 (ttt90) REVERT: C 101 MET cc_start: 0.7716 (mtt) cc_final: 0.7371 (mtt) REVERT: C 134 ARG cc_start: 0.6830 (pmt-80) cc_final: 0.6443 (pmt-80) REVERT: C 195 ASP cc_start: 0.7338 (p0) cc_final: 0.7110 (p0) REVERT: C 258 ASP cc_start: 0.7199 (t70) cc_final: 0.6290 (t0) REVERT: C 285 LEU cc_start: 0.8177 (tt) cc_final: 0.7942 (tt) REVERT: R 49 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8365 (mp) REVERT: R 51 LEU cc_start: 0.8007 (mt) cc_final: 0.7675 (mp) REVERT: R 73 PHE cc_start: 0.8142 (t80) cc_final: 0.7894 (t80) REVERT: R 76 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7341 (mm) outliers start: 15 outliers final: 12 residues processed: 158 average time/residue: 0.2728 time to fit residues: 52.8310 Evaluate side-chains 164 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099541 restraints weight = 9386.702| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.28 r_work: 0.3099 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6578 Z= 0.239 Angle : 0.529 8.012 8964 Z= 0.268 Chirality : 0.042 0.160 1061 Planarity : 0.004 0.042 1122 Dihedral : 5.167 102.393 917 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 18.97 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.30), residues: 844 helix: 1.70 (0.29), residues: 364 sheet: -0.05 (0.41), residues: 163 loop : -1.23 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 158 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE R 178 TYR 0.009 0.001 TYR C 59 ARG 0.010 0.001 ARG B 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.18 seconds wall clock time: 38 minutes 42.17 seconds (2322.17 seconds total)