Starting phenix.real_space_refine (version: dev) on Mon Dec 12 00:44:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2022/8dwg_27753_updated.pdb" } resolution = 2.71 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= 0.001 sd= 0.024 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 "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B TYR 243": "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 83": "OD1" <-> "OD2" 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 163": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 322": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R PHE 75": "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 PHE 186": "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 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 90": "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 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8350 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 124 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 240} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'U39': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.62 Number of scatterers: 8350 At special positions: 0 Unit cell: (97.68, 116.16, 120.56, 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 57 16.00 O 1516 8.00 N 1421 7.00 C 5356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 251 " distance=2.03 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 33.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.536A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.536A 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 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.582A pdb=" N LEU B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 127 " --> pdb=" O ASP B 124 " (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 154 removed outlier: 3.637A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' 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 203 removed outlier: 3.574A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (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 36 removed outlier: 3.626A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'R' and resid 24 through 52 removed outlier: 3.904A pdb=" N LEU R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER R 29 " --> pdb=" O LYS R 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 87 removed outlier: 3.754A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 97 removed outlier: 3.561A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 93 through 97' Processing helix chain 'R' and resid 99 through 125 removed outlier: 4.801A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 138 through 160 Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 212 through 228 Processing helix chain 'R' and resid 231 through 238 removed outlier: 6.192A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 251 removed outlier: 3.899A pdb=" N PHE R 250 " --> pdb=" O ARG R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 272 Proline residue: R 269 - end of helix 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 sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 6.830A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.979A 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: 6.967A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.206A 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: 6.806A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.959A 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: 6.822A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.235A 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: 6.632A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.763A 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: 6.514A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.393A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.223A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.297A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 147 378 hydrogen bonds defined for protein. 1059 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: 2.76 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2668 1.34 - 1.46: 1972 1.46 - 1.58: 3819 1.58 - 1.69: 1 1.69 - 1.81: 77 Bond restraints: 8537 Sorted by residual: bond pdb=" C1 U39 R 401 " pdb=" N1 U39 R 401 " ideal model delta sigma weight residual 1.465 1.354 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" N2 U39 R 401 " pdb=" S1 U39 R 401 " ideal model delta sigma weight residual 1.723 1.627 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C11 U39 R 401 " pdb=" N2 U39 R 401 " ideal model delta sigma weight residual 1.471 1.379 0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C12 U39 R 401 " pdb=" S1 U39 R 401 " ideal model delta sigma weight residual 1.832 1.754 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C2 U39 R 401 " pdb=" N1 U39 R 401 " ideal model delta sigma weight residual 1.470 1.413 0.057 2.00e-02 2.50e+03 8.24e+00 ... (remaining 8532 not shown) Histogram of bond angle deviations from ideal: 59.96 - 74.79: 3 74.79 - 89.61: 0 89.61 - 104.44: 88 104.44 - 119.27: 6893 119.27 - 134.10: 4635 Bond angle restraints: 11619 Sorted by residual: angle pdb=" O3 U39 R 401 " pdb=" S1 U39 R 401 " pdb=" O4 U39 R 401 " ideal model delta sigma weight residual 101.20 119.19 -17.99 3.00e+00 1.11e-01 3.59e+01 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.46 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 109.81 116.34 -6.53 2.21e+00 2.05e-01 8.72e+00 angle pdb=" C HIS R 243 " pdb=" N VAL R 244 " pdb=" CA VAL R 244 " ideal model delta sigma weight residual 122.97 120.08 2.89 9.80e-01 1.04e+00 8.72e+00 angle pdb=" C THR B 216 " pdb=" N CYS B 217 " pdb=" CA CYS B 217 " ideal model delta sigma weight residual 121.54 116.12 5.42 1.91e+00 2.74e-01 8.06e+00 ... (remaining 11614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4565 17.46 - 34.92: 329 34.92 - 52.37: 59 52.37 - 69.83: 4 69.83 - 87.29: 5 Dihedral angle restraints: 4962 sinusoidal: 1772 harmonic: 3190 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 141.76 -48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1208 0.073 - 0.147: 132 0.147 - 0.220: 4 0.220 - 0.294: 0 0.294 - 0.367: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" C12 U39 R 401 " pdb=" C13 U39 R 401 " pdb=" C14 U39 R 401 " pdb=" S1 U39 R 401 " both_signs ideal model delta sigma weight residual True 3.22 -2.86 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CG LEU B 143 " pdb=" CB LEU B 143 " pdb=" CD1 LEU B 143 " pdb=" CD2 LEU B 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB THR C 223 " pdb=" CA THR C 223 " pdb=" OG1 THR C 223 " pdb=" CG2 THR C 223 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1342 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U39 R 401 " -0.058 2.00e-02 2.50e+03 9.95e-02 1.24e+02 pdb=" C10 U39 R 401 " 0.094 2.00e-02 2.50e+03 pdb=" C2 U39 R 401 " 0.119 2.00e-02 2.50e+03 pdb=" N1 U39 R 401 " -0.152 2.00e-02 2.50e+03 pdb=" O1 U39 R 401 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO D 49 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 48 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ASP D 48 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP D 48 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO D 49 " -0.012 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 131 2.66 - 3.22: 7698 3.22 - 3.78: 12701 3.78 - 4.34: 18186 4.34 - 4.90: 30422 Nonbonded interactions: 69138 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O PHE R 232 " model vdw 2.106 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR B 243 " pdb=" OH TYR R 130 " model vdw 2.177 2.440 nonbonded pdb=" OE2 GLU B 25 " pdb=" NZ LYS B 29 " model vdw 2.199 2.520 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.227 2.520 ... (remaining 69133 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 57 5.16 5 C 5356 2.51 5 N 1421 2.21 5 O 1516 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: 0.870 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: 5.630 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 26.700 Find NCS groups from input model: 0.260 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.006 0.111 8537 Z= 0.417 Angle : 0.640 17.986 11619 Z= 0.349 Chirality : 0.046 0.367 1345 Planarity : 0.005 0.100 1456 Dihedral : 12.646 87.290 2893 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1081 helix: -1.23 (0.24), residues: 367 sheet: 0.27 (0.31), residues: 281 loop : -0.85 (0.30), residues: 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.962 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.9576 time to fit residues: 191.8719 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 80 ASN B 82 HIS B 101 ASN B 144 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 340 ASN E 39 GLN E 82 GLN E 167 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8537 Z= 0.212 Angle : 0.542 6.061 11619 Z= 0.293 Chirality : 0.042 0.138 1345 Planarity : 0.004 0.041 1456 Dihedral : 5.402 87.316 1188 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.26), residues: 1081 helix: 0.95 (0.27), residues: 363 sheet: 0.52 (0.30), residues: 286 loop : -0.80 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 1.056 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 183 average time/residue: 1.1408 time to fit residues: 222.8774 Evaluate side-chains 178 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0743 time to fit residues: 1.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 0.0040 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN B 144 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 220 GLN C 237 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8537 Z= 0.225 Angle : 0.534 10.407 11619 Z= 0.282 Chirality : 0.042 0.148 1345 Planarity : 0.004 0.035 1456 Dihedral : 5.239 85.946 1188 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.62 (0.26), residues: 1081 helix: 1.76 (0.28), residues: 361 sheet: 0.49 (0.29), residues: 292 loop : -0.78 (0.31), residues: 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.014 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 176 average time/residue: 1.0959 time to fit residues: 206.2022 Evaluate side-chains 173 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1260 time to fit residues: 1.9001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8537 Z= 0.220 Angle : 0.523 11.697 11619 Z= 0.277 Chirality : 0.042 0.152 1345 Planarity : 0.004 0.033 1456 Dihedral : 5.133 85.506 1188 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.75 (0.26), residues: 1081 helix: 2.01 (0.28), residues: 362 sheet: 0.40 (0.29), residues: 293 loop : -0.74 (0.31), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.020 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 178 average time/residue: 1.1540 time to fit residues: 219.0659 Evaluate side-chains 177 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 6 average time/residue: 0.3279 time to fit residues: 3.7002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0970 chunk 59 optimal weight: 0.0470 chunk 1 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8537 Z= 0.149 Angle : 0.484 9.707 11619 Z= 0.257 Chirality : 0.041 0.152 1345 Planarity : 0.003 0.033 1456 Dihedral : 4.949 87.326 1188 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1081 helix: 2.27 (0.28), residues: 362 sheet: 0.46 (0.29), residues: 292 loop : -0.76 (0.31), residues: 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 0.960 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 182 average time/residue: 1.1390 time to fit residues: 221.0680 Evaluate side-chains 185 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.1463 time to fit residues: 2.6781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN C 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8537 Z= 0.147 Angle : 0.482 10.312 11619 Z= 0.254 Chirality : 0.040 0.134 1345 Planarity : 0.003 0.034 1456 Dihedral : 4.881 88.113 1188 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.93 (0.26), residues: 1081 helix: 2.33 (0.28), residues: 362 sheet: 0.46 (0.29), residues: 281 loop : -0.74 (0.30), residues: 438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.038 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 184 average time/residue: 1.0956 time to fit residues: 215.5407 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1272 time to fit residues: 1.5512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8537 Z= 0.258 Angle : 0.541 10.841 11619 Z= 0.284 Chirality : 0.042 0.136 1345 Planarity : 0.004 0.036 1456 Dihedral : 5.091 86.370 1188 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.80 (0.26), residues: 1081 helix: 2.16 (0.28), residues: 362 sheet: 0.42 (0.30), residues: 281 loop : -0.77 (0.30), residues: 438 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 0.973 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 175 average time/residue: 1.0861 time to fit residues: 202.8356 Evaluate side-chains 177 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.4589 time to fit residues: 4.4037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 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 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8537 Z= 0.248 Angle : 0.540 11.079 11619 Z= 0.285 Chirality : 0.042 0.136 1345 Planarity : 0.004 0.049 1456 Dihedral : 5.121 86.397 1188 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.26), residues: 1081 helix: 2.10 (0.28), residues: 362 sheet: 0.41 (0.29), residues: 281 loop : -0.78 (0.30), residues: 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 0.959 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 178 average time/residue: 1.1246 time to fit residues: 213.5564 Evaluate side-chains 178 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.6411 time to fit residues: 2.7368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8537 Z= 0.264 Angle : 0.556 12.476 11619 Z= 0.291 Chirality : 0.043 0.136 1345 Planarity : 0.004 0.059 1456 Dihedral : 5.157 86.028 1188 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.26), residues: 1081 helix: 2.01 (0.28), residues: 364 sheet: 0.39 (0.29), residues: 281 loop : -0.74 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 0.881 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 179 average time/residue: 1.1580 time to fit residues: 221.2890 Evaluate side-chains 181 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.4182 time to fit residues: 3.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8537 Z= 0.230 Angle : 0.540 11.977 11619 Z= 0.283 Chirality : 0.042 0.136 1345 Planarity : 0.004 0.062 1456 Dihedral : 5.122 86.613 1188 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.26), residues: 1081 helix: 2.03 (0.28), residues: 364 sheet: 0.37 (0.29), residues: 286 loop : -0.72 (0.31), residues: 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.977 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 174 average time/residue: 1.1309 time to fit residues: 210.2161 Evaluate side-chains 176 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.1409 time to fit residues: 1.8883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097016 restraints weight = 11778.060| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.60 r_work: 0.3151 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8537 Z= 0.239 Angle : 0.544 11.445 11619 Z= 0.284 Chirality : 0.042 0.134 1345 Planarity : 0.004 0.065 1456 Dihedral : 5.125 86.306 1188 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.26), residues: 1081 helix: 2.02 (0.28), residues: 364 sheet: 0.37 (0.29), residues: 286 loop : -0.69 (0.31), residues: 431 =============================================================================== Job complete usr+sys time: 3807.83 seconds wall clock time: 67 minutes 59.83 seconds (4079.83 seconds total)