Starting phenix.real_space_refine on Tue Nov 14 09:22:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/11_2023/8dwc_27752.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/11_2023/8dwc_27752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/11_2023/8dwc_27752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/11_2023/8dwc_27752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/11_2023/8dwc_27752.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/11_2023/8dwc_27752.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5318 2.51 5 N 1413 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 21": "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 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "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 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "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 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 PHE 200": "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" 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 ARG 117": "NH1" <-> "NH2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 8298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 109 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 10} 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: "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: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1925 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 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: "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 Time building chain proxies: 4.79, per 1000 atoms: 0.58 Number of scatterers: 8298 At special positions: 0 Unit cell: (104.72, 115.28, 118.8, 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 56 16.00 O 1511 8.00 N 1413 7.00 C 5318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.667A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.559A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.503A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.565A pdb=" N GLY R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 3.686A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.991A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 4.759A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 170 through 204 removed outlier: 3.807A pdb=" N GLN R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER R 176 " --> pdb=" O TRP R 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 227 Processing helix chain 'R' and resid 230 through 239 removed outlier: 3.607A pdb=" N ILE R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 253 through 273 Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.191A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.518A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.997A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.622A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.965A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.779A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.133A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.620A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.533A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.729A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.180A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.896A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.657A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.647A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.538A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.515A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.663A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR E 94 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA E 92 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.556A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.597A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1176 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: 2.47 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2603 1.33 - 1.45: 1529 1.45 - 1.57: 4274 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8482 Sorted by residual: bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.19e+00 bond pdb=" N THR B 221 " pdb=" CA THR B 221 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.37e-02 5.33e+03 4.69e+00 bond pdb=" N ALA B 218 " pdb=" CA ALA B 218 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.33e-02 5.65e+03 3.86e+00 bond pdb=" CG1 ILE B 49 " pdb=" CD1 ILE B 49 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.46e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.81: 117 105.81 - 112.88: 4610 112.88 - 119.95: 2693 119.95 - 127.02: 4023 127.02 - 134.09: 102 Bond angle restraints: 11545 Sorted by residual: angle pdb=" N THR B 221 " pdb=" CA THR B 221 " pdb=" C THR B 221 " ideal model delta sigma weight residual 113.72 109.31 4.41 1.30e+00 5.92e-01 1.15e+01 angle pdb=" N ALA B 218 " pdb=" CA ALA B 218 " pdb=" C ALA B 218 " ideal model delta sigma weight residual 113.23 109.46 3.77 1.24e+00 6.50e-01 9.26e+00 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 112.80 109.75 3.05 1.15e+00 7.56e-01 7.03e+00 angle pdb=" CA ASP B 220 " pdb=" C ASP B 220 " pdb=" O ASP B 220 " ideal model delta sigma weight residual 120.92 118.34 2.58 1.14e+00 7.69e-01 5.13e+00 angle pdb=" C ASP B 42 " pdb=" N ASN B 43 " pdb=" CA ASN B 43 " ideal model delta sigma weight residual 124.82 128.66 -3.84 1.78e+00 3.16e-01 4.66e+00 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4465 15.94 - 31.87: 379 31.87 - 47.81: 78 47.81 - 63.74: 10 63.74 - 79.68: 3 Dihedral angle restraints: 4935 sinusoidal: 1742 harmonic: 3193 Sorted by residual: 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 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP C 258 " pdb=" C ASP C 258 " pdb=" N GLN C 259 " pdb=" CA GLN C 259 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 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 93.00 125.65 -32.65 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 872 0.042 - 0.084: 349 0.084 - 0.126: 109 0.126 - 0.168: 9 0.168 - 0.210: 3 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL B 109 " pdb=" CA VAL B 109 " pdb=" CG1 VAL B 109 " pdb=" CG2 VAL B 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+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 9.81e-01 chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1339 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 217 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C CYS B 217 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS B 217 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 218 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " 0.012 2.00e-02 2.50e+03 1.37e-02 2.82e+00 pdb=" CG HIS B 209 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.004 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 111 2.66 - 3.22: 7580 3.22 - 3.78: 12389 3.78 - 4.34: 17741 4.34 - 4.90: 29887 Nonbonded interactions: 67708 Sorted by model distance: nonbonded pdb=" OH TYR R 130 " pdb=" OH TYR B 243 " model vdw 2.095 2.440 nonbonded pdb=" NH2 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.123 2.520 nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.149 2.520 nonbonded pdb=" OD2 ASP R 177 " pdb=" NE1 TRP R 241 " model vdw 2.229 2.520 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.232 2.440 ... (remaining 67703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.110 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.008 0.073 8482 Z= 0.503 Angle : 0.645 7.370 11545 Z= 0.354 Chirality : 0.047 0.210 1342 Planarity : 0.004 0.044 1448 Dihedral : 12.543 79.679 2867 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.24), residues: 1082 helix: -1.16 (0.24), residues: 365 sheet: 0.11 (0.31), residues: 282 loop : -0.78 (0.30), residues: 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.937 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 1.0512 time to fit residues: 227.3262 Evaluate side-chains 187 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.251 Angle : 0.567 8.391 11545 Z= 0.299 Chirality : 0.043 0.162 1342 Planarity : 0.004 0.038 1448 Dihedral : 4.534 17.774 1181 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.94 % Allowed : 11.22 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.16 (0.25), residues: 1082 helix: 1.00 (0.27), residues: 349 sheet: 0.25 (0.31), residues: 288 loop : -0.62 (0.30), residues: 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 0.864 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 191 average time/residue: 1.0858 time to fit residues: 222.2085 Evaluate side-chains 186 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 3 average time/residue: 0.1417 time to fit residues: 1.8567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 176 GLN C 220 GLN R 133 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8482 Z= 0.259 Angle : 0.552 9.133 11545 Z= 0.287 Chirality : 0.043 0.202 1342 Planarity : 0.004 0.039 1448 Dihedral : 4.348 16.958 1181 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.42 % Allowed : 14.52 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.59 (0.26), residues: 1082 helix: 1.70 (0.27), residues: 349 sheet: 0.37 (0.31), residues: 290 loop : -0.61 (0.30), residues: 443 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 0.936 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 201 average time/residue: 1.0054 time to fit residues: 217.7378 Evaluate side-chains 197 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 2 average time/residue: 0.8892 time to fit residues: 3.1378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN C 176 GLN B 22 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8482 Z= 0.200 Angle : 0.506 8.442 11545 Z= 0.267 Chirality : 0.042 0.183 1342 Planarity : 0.004 0.034 1448 Dihedral : 4.161 15.788 1181 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 15.82 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1082 helix: 2.15 (0.27), residues: 349 sheet: 0.35 (0.30), residues: 295 loop : -0.57 (0.30), residues: 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 0.975 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 196 average time/residue: 1.0406 time to fit residues: 219.4696 Evaluate side-chains 196 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.1449 time to fit residues: 2.6571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.246 Angle : 0.527 9.000 11545 Z= 0.276 Chirality : 0.042 0.185 1342 Planarity : 0.004 0.048 1448 Dihedral : 4.166 15.793 1181 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.01 % Allowed : 17.12 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.95 (0.26), residues: 1082 helix: 2.24 (0.27), residues: 353 sheet: 0.47 (0.30), residues: 290 loop : -0.57 (0.30), residues: 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.954 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 199 average time/residue: 0.9914 time to fit residues: 212.1351 Evaluate side-chains 197 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1029 time to fit residues: 1.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN C 176 GLN R 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.237 Angle : 0.525 8.778 11545 Z= 0.273 Chirality : 0.042 0.183 1342 Planarity : 0.004 0.048 1448 Dihedral : 4.138 15.899 1181 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 18.18 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.03 (0.26), residues: 1082 helix: 2.34 (0.27), residues: 354 sheet: 0.44 (0.30), residues: 292 loop : -0.51 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 0.893 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 204 average time/residue: 0.9746 time to fit residues: 214.3123 Evaluate side-chains 201 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1112 time to fit residues: 1.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN R 67 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8482 Z= 0.224 Angle : 0.514 8.685 11545 Z= 0.271 Chirality : 0.042 0.182 1342 Planarity : 0.004 0.051 1448 Dihedral : 4.112 15.655 1181 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.01 % Allowed : 18.65 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1082 helix: 2.46 (0.27), residues: 354 sheet: 0.41 (0.30), residues: 285 loop : -0.51 (0.30), residues: 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 0.943 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 206 average time/residue: 0.9896 time to fit residues: 219.6435 Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1140 time to fit residues: 1.8798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 82 optimal weight: 0.0870 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 0.0070 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 220 GLN R 67 ASN B 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8482 Z= 0.133 Angle : 0.475 8.127 11545 Z= 0.253 Chirality : 0.040 0.184 1342 Planarity : 0.004 0.047 1448 Dihedral : 3.876 14.893 1181 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.18 % Allowed : 19.01 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.32 (0.26), residues: 1082 helix: 2.72 (0.28), residues: 356 sheet: 0.54 (0.31), residues: 276 loop : -0.39 (0.30), residues: 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 0.930 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 215 average time/residue: 1.0293 time to fit residues: 240.4597 Evaluate side-chains 193 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1458 time to fit residues: 1.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 132 ASN C 220 GLN R 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8482 Z= 0.256 Angle : 0.532 8.150 11545 Z= 0.277 Chirality : 0.042 0.174 1342 Planarity : 0.004 0.042 1448 Dihedral : 4.045 15.121 1181 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.94 % Allowed : 19.83 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.19 (0.26), residues: 1082 helix: 2.59 (0.27), residues: 356 sheet: 0.54 (0.31), residues: 275 loop : -0.50 (0.30), residues: 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 0.937 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 203 average time/residue: 1.0476 time to fit residues: 228.6471 Evaluate side-chains 198 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1635 time to fit residues: 1.6890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 132 ASN C 220 GLN R 67 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8482 Z= 0.172 Angle : 0.494 8.235 11545 Z= 0.261 Chirality : 0.041 0.179 1342 Planarity : 0.003 0.040 1448 Dihedral : 3.984 14.883 1181 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.94 % Allowed : 19.83 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.28 (0.26), residues: 1082 helix: 2.65 (0.27), residues: 357 sheet: 0.53 (0.31), residues: 277 loop : -0.41 (0.30), residues: 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 0.990 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 202 average time/residue: 1.0027 time to fit residues: 218.5205 Evaluate side-chains 198 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.9824 time to fit residues: 4.4368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 220 GLN R 67 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100696 restraints weight = 11785.383| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.75 r_work: 0.3163 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8482 Z= 0.174 Angle : 0.504 8.708 11545 Z= 0.264 Chirality : 0.041 0.173 1342 Planarity : 0.004 0.059 1448 Dihedral : 3.931 14.622 1181 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.59 % Allowed : 20.19 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.33 (0.26), residues: 1082 helix: 2.74 (0.27), residues: 356 sheet: 0.58 (0.31), residues: 276 loop : -0.44 (0.30), residues: 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3914.24 seconds wall clock time: 70 minutes 5.19 seconds (4205.19 seconds total)