Starting phenix.real_space_refine (version: dev) on Thu May 12 20:40:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8p_24900/05_2022/7s8p_24900_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.026 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "R PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 82": "NH1" <-> "NH2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8093 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 97 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: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 220, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1858 Unusual residues: {'8IX': 1} Classifications: {'undetermined': 1, 'peptide': 247} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 238, None: 1} Not linked: pdbres="GLN R 280 " pdbres="8IX R 401 " Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 5.05, per 1000 atoms: 0.62 Number of scatterers: 8093 At special positions: 0 Unit cell: (89.18, 117.39, 130.13, 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 54 16.00 O 1474 8.00 N 1383 7.00 C 5182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.04 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: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 13 sheets defined 33.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.680A pdb=" N ALA B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.882A pdb=" N LEU B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 122 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 123 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 128 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N ALA B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) 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 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 201 removed outlier: 3.733A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 195 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 removed outlier: 3.521A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 23 removed outlier: 3.514A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.282A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' 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 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 27 through 51 removed outlier: 3.507A pdb=" N ILE R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL R 40 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 86 removed outlier: 3.620A pdb=" N PHE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU R 83 " --> pdb=" O GLN R 79 " (cutoff:3.500A) Proline residue: R 84 - end of helix Processing helix chain 'R' and resid 92 through 109 removed outlier: 3.975A pdb=" N LYS R 96 " --> pdb=" O HIS R 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL R 99 " --> pdb=" O ARG R 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 101 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE R 104 " --> pdb=" O SER R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix removed outlier: 3.726A pdb=" N THR R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 125 removed outlier: 3.750A pdb=" N THR R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 removed outlier: 3.544A pdb=" N ARG R 131 " --> pdb=" O PRO R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 156 removed outlier: 4.294A pdb=" N SER R 139 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL R 141 " --> pdb=" O LEU R 138 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL R 142 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL R 144 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY R 148 " --> pdb=" O LEU R 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU R 149 " --> pdb=" O LEU R 146 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU R 151 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 152 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE R 153 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET R 155 " --> pdb=" O LEU R 152 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 156 " --> pdb=" O PHE R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 203 Proline residue: R 180 - end of helix removed outlier: 3.908A pdb=" N ILE R 185 " --> pdb=" O ALA R 182 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE R 186 " --> pdb=" O TRP R 183 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 191 " --> pdb=" O CYS R 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL R 193 " --> pdb=" O VAL R 190 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER R 194 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER R 195 " --> pdb=" O CYS R 192 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 197 " --> pdb=" O SER R 194 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU R 198 " --> pdb=" O SER R 195 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG R 201 " --> pdb=" O LEU R 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE R 202 " --> pdb=" O LEU R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 228 removed outlier: 4.329A pdb=" N THR R 212 " --> pdb=" O MET R 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR R 215 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL R 216 " --> pdb=" O ARG R 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE R 218 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU R 219 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU R 223 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL R 224 " --> pdb=" O THR R 221 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE R 225 " --> pdb=" O VAL R 222 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 227 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS R 228 " --> pdb=" O PHE R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 235 Processing helix chain 'R' and resid 248 through 250 No H-bonds generated for 'chain 'R' and resid 248 through 250' Processing helix chain 'R' and resid 253 through 266 removed outlier: 3.606A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 272 Processing helix chain 'R' and resid 274 through 279 Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 6.998A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.902A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.917A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.891A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.817A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.909A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.331A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.780A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.680A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 114 through 117 removed outlier: 3.573A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.728A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'E' and resid 213 through 219 removed outlier: 3.794A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 711 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: 2.15 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1288 1.31 - 1.44: 2305 1.44 - 1.57: 4591 1.57 - 1.70: 5 1.70 - 1.83: 74 Bond restraints: 8263 Sorted by residual: bond pdb=" C08 8IX R 401 " pdb=" C09 8IX R 401 " ideal model delta sigma weight residual 0.014 1.482 -1.468 2.00e-02 2.50e+03 5.39e+03 bond pdb=" C10 8IX R 401 " pdb=" C12 8IX R 401 " ideal model delta sigma weight residual 0.546 1.517 -0.971 2.00e-02 2.50e+03 2.35e+03 bond pdb=" C14 8IX R 401 " pdb=" C15 8IX R 401 " ideal model delta sigma weight residual 0.966 1.609 -0.643 2.00e-02 2.50e+03 1.03e+03 bond pdb=" C10 8IX R 401 " pdb=" C15 8IX R 401 " ideal model delta sigma weight residual 1.068 1.572 -0.504 2.00e-02 2.50e+03 6.36e+02 bond pdb=" C09 8IX R 401 " pdb=" C10 8IX R 401 " ideal model delta sigma weight residual 1.989 1.528 0.461 2.00e-02 2.50e+03 5.31e+02 ... (remaining 8258 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 116 105.52 - 112.66: 4370 112.66 - 119.80: 2612 119.80 - 126.94: 4068 126.94 - 134.07: 99 Bond angle restraints: 11265 Sorted by residual: angle pdb=" C06 8IX R 401 " pdb=" C12 8IX R 401 " pdb=" C10 8IX R 401 " ideal model delta sigma weight residual 93.64 111.14 -17.50 3.00e+00 1.11e-01 3.40e+01 angle pdb=" C12 8IX R 401 " pdb=" C10 8IX R 401 " pdb=" C15 8IX R 401 " ideal model delta sigma weight residual 123.69 106.94 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C06 8IX R 401 " pdb=" C17 8IX R 401 " pdb=" C14 8IX R 401 " ideal model delta sigma weight residual 95.04 110.49 -15.45 3.00e+00 1.11e-01 2.65e+01 angle pdb=" C15 8IX R 401 " pdb=" C14 8IX R 401 " pdb=" C17 8IX R 401 " ideal model delta sigma weight residual 94.18 109.26 -15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C11 8IX R 401 " pdb=" C10 8IX R 401 " pdb=" C15 8IX R 401 " ideal model delta sigma weight residual 98.19 112.50 -14.31 3.00e+00 1.11e-01 2.27e+01 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 4329 15.19 - 30.37: 372 30.37 - 45.56: 91 45.56 - 60.74: 15 60.74 - 75.93: 7 Dihedral angle restraints: 4814 sinusoidal: 1661 harmonic: 3153 Sorted by residual: dihedral pdb=" CA TYR B 243 " pdb=" C TYR B 243 " pdb=" N ASN B 244 " pdb=" CA ASN B 244 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU C 130 " pdb=" C GLU C 130 " pdb=" N GLY C 131 " pdb=" CA GLY C 131 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.164: 1328 1.164 - 2.328: 0 2.328 - 3.492: 1 3.492 - 4.656: 0 4.656 - 5.820: 1 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C10 8IX R 401 " pdb=" C09 8IX R 401 " pdb=" C11 8IX R 401 " pdb=" C15 8IX R 401 " both_signs ideal model delta sigma weight residual False -2.83 2.99 -5.82 2.00e-01 2.50e+01 8.47e+02 chirality pdb=" C08 8IX R 401 " pdb=" C07 8IX R 401 " pdb=" C09 8IX R 401 " pdb=" C13 8IX R 401 " both_signs ideal model delta sigma weight residual False -0.04 -2.71 2.67 2.00e-01 2.50e+01 1.78e+02 chirality pdb=" C14 8IX R 401 " pdb=" C13 8IX R 401 " pdb=" C15 8IX R 401 " pdb=" C17 8IX R 401 " both_signs ideal model delta sigma weight residual False -2.07 -3.17 1.09 2.00e-01 2.50e+01 3.00e+01 ... (remaining 1327 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO E 107 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 213 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 49 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.024 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 336 2.73 - 3.27: 7508 3.27 - 3.81: 11764 3.81 - 4.36: 14821 4.36 - 4.90: 26345 Nonbonded interactions: 60774 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O GLY R 229 " model vdw 2.183 2.440 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.208 2.520 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASP B 20 " pdb=" NZ LYS C 89 " model vdw 2.289 2.520 nonbonded pdb=" NH2 ARG E 67 " pdb=" OD2 ASP E 90 " model vdw 2.305 2.520 ... (remaining 60769 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5182 2.51 5 N 1383 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.760 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: 0.000 Extract box with map and model: 4.100 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 24.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.024 1.468 8263 Z= 1.627 Angle : 0.855 17.502 11265 Z= 0.412 Chirality : 0.184 5.820 1330 Planarity : 0.004 0.045 1417 Dihedral : 12.773 75.928 2769 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.01 (0.23), residues: 1071 helix: -1.79 (0.24), residues: 350 sheet: 0.15 (0.32), residues: 253 loop : -1.72 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.888 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.0364 time to fit residues: 199.3226 Evaluate side-chains 166 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 340 ASN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.150 8263 Z= 0.356 Angle : 0.948 22.672 11265 Z= 0.452 Chirality : 0.133 4.554 1330 Planarity : 0.006 0.104 1417 Dihedral : 5.135 25.783 1169 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.30 (0.24), residues: 1071 helix: -0.77 (0.26), residues: 349 sheet: 0.34 (0.31), residues: 274 loop : -1.65 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.957 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 1.0276 time to fit residues: 185.4755 Evaluate side-chains 168 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 0.1081 time to fit residues: 2.2725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 340 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.150 8263 Z= 0.359 Angle : 0.951 22.672 11265 Z= 0.455 Chirality : 0.133 4.554 1330 Planarity : 0.006 0.132 1417 Dihedral : 5.135 25.783 1169 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.30 (0.24), residues: 1071 helix: -0.77 (0.26), residues: 349 sheet: 0.34 (0.31), residues: 274 loop : -1.65 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.018 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 1.0869 time to fit residues: 187.8361 Evaluate side-chains 160 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 340 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.150 8263 Z= 0.359 Angle : 0.951 22.671 11265 Z= 0.455 Chirality : 0.133 4.554 1330 Planarity : 0.006 0.132 1417 Dihedral : 5.135 25.783 1169 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.30 (0.24), residues: 1071 helix: -0.77 (0.26), residues: 349 sheet: 0.34 (0.31), residues: 274 loop : -1.65 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.997 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 1.0673 time to fit residues: 182.0376 Evaluate side-chains 160 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 340 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.151 8263 Z= 0.359 Angle : 0.951 22.662 11265 Z= 0.455 Chirality : 0.133 4.554 1330 Planarity : 0.006 0.132 1417 Dihedral : 5.135 25.783 1169 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.30 (0.24), residues: 1071 helix: -0.77 (0.26), residues: 349 sheet: 0.34 (0.31), residues: 274 loop : -1.65 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.990 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 1.1034 time to fit residues: 188.1450 Evaluate side-chains 160 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.0070 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 340 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.151 8263 Z= 0.358 Angle : 0.950 22.509 11265 Z= 0.455 Chirality : 0.133 4.554 1330 Planarity : 0.006 0.131 1417 Dihedral : 5.135 25.782 1169 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.30 (0.24), residues: 1071 helix: -0.76 (0.26), residues: 349 sheet: 0.34 (0.31), residues: 274 loop : -1.65 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 0.926 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 1.0528 time to fit residues: 180.8541 Evaluate side-chains 160 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 75 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 223 ASN C 156 GLN C 340 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.144 8263 Z= 0.233 Angle : 0.841 31.660 11265 Z= 0.379 Chirality : 0.113 3.783 1330 Planarity : 0.005 0.082 1417 Dihedral : 4.858 22.053 1169 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1071 helix: -0.45 (0.27), residues: 348 sheet: 0.47 (0.30), residues: 279 loop : -1.66 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 0.952 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 167 average time/residue: 1.0762 time to fit residues: 191.2913 Evaluate side-chains 167 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0714 time to fit residues: 1.5566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 65 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 144 ASN B 223 ASN C 156 GLN C 268 ASN C 340 ASN E 77 ASN E 174 GLN R 45 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.156 8263 Z= 0.233 Angle : 0.777 28.214 11265 Z= 0.352 Chirality : 0.120 4.066 1330 Planarity : 0.006 0.109 1417 Dihedral : 4.661 18.970 1169 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1071 helix: -0.22 (0.27), residues: 348 sheet: 0.45 (0.31), residues: 277 loop : -1.61 (0.27), residues: 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 0.740 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 165 average time/residue: 1.1741 time to fit residues: 207.3466 Evaluate side-chains 170 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 0.2009 time to fit residues: 2.3413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 223 ASN C 156 GLN E 77 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.152 8263 Z= 0.263 Angle : 0.801 30.423 11265 Z= 0.362 Chirality : 0.117 3.941 1330 Planarity : 0.005 0.107 1417 Dihedral : 4.660 18.406 1169 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.89 (0.25), residues: 1071 helix: -0.20 (0.27), residues: 348 sheet: 0.57 (0.31), residues: 270 loop : -1.60 (0.27), residues: 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.942 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 168 average time/residue: 1.1182 time to fit residues: 200.0802 Evaluate side-chains 169 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2345 time to fit residues: 1.6020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 223 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.151 8263 Z= 0.295 Angle : 0.815 29.677 11265 Z= 0.372 Chirality : 0.118 3.978 1330 Planarity : 0.005 0.113 1417 Dihedral : 4.709 18.373 1169 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1071 helix: -0.14 (0.27), residues: 348 sheet: 0.54 (0.31), residues: 276 loop : -1.60 (0.27), residues: 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 0.917 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 171 average time/residue: 1.1104 time to fit residues: 201.9524 Evaluate side-chains 171 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4726 time to fit residues: 2.8400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 223 ASN B 239 ASN C 156 GLN E 77 ASN E 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098816 restraints weight = 11229.610| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.66 r_work: 0.3267 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.3238 rms_B_bonded: 1.54 restraints_weight: 0.1250 r_work: 0.3221 rms_B_bonded: 1.68 restraints_weight: 0.0625 r_work: 0.3202 rms_B_bonded: 1.89 restraints_weight: 0.0312 r_work: 0.3180 rms_B_bonded: 2.15 restraints_weight: 0.0156 r_work: 0.3156 rms_B_bonded: 2.48 restraints_weight: 0.0078 r_work: 0.3127 rms_B_bonded: 2.90 restraints_weight: 0.0039 r_work: 0.3093 rms_B_bonded: 3.42 restraints_weight: 0.0020 r_work: 0.3054 rms_B_bonded: 4.06 restraints_weight: 0.0010 r_work: 0.3007 rms_B_bonded: 4.85 restraints_weight: 0.0005 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.151 8263 Z= 0.231 Angle : 0.775 29.965 11265 Z= 0.350 Chirality : 0.117 3.948 1330 Planarity : 0.005 0.109 1417 Dihedral : 4.571 18.159 1169 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.77 (0.25), residues: 1071 helix: 0.01 (0.28), residues: 348 sheet: 0.50 (0.31), residues: 277 loop : -1.55 (0.27), residues: 446 =============================================================================== Job complete usr+sys time: 3302.84 seconds wall clock time: 59 minutes 0.15 seconds (3540.15 seconds total)