Starting phenix.real_space_refine (version: dev) on Mon Feb 20 07:03:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnq_12232/02_2023/7bnq_12232.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnq_12232/02_2023/7bnq_12232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnq_12232/02_2023/7bnq_12232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnq_12232/02_2023/7bnq_12232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnq_12232/02_2023/7bnq_12232.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnq_12232/02_2023/7bnq_12232.pdb" } resolution = 4.1 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= 0.004 sd= 0.044 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 Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 797": "OD1" <-> "OD2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11617 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 6020 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 27, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2784 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain: "C" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 408 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1760 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Time building chain proxies: 6.71, per 1000 atoms: 0.58 Number of scatterers: 11617 At special positions: 0 Unit cell: (119.84, 126.26, 99.51, 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 32 16.00 O 2279 8.00 N 1983 7.00 C 7323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 665 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 22.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.646A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.514A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 215 through 231 removed outlier: 4.268A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.867A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 316 removed outlier: 3.840A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 Processing helix chain 'A' and resid 497 through 500 removed outlier: 3.728A pdb=" N ASP A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.816A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 332 through 336 removed outlier: 4.148A pdb=" N GLY B 335 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.642A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 62 removed outlier: 3.714A pdb=" N TYR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.655A pdb=" N VAL D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.813A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 4.087A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 129' Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.798A pdb=" N LYS D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.569A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.566A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 213 Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.711A pdb=" N ARG D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 240 Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 54 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 7.014A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 89 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 99 removed outlier: 7.308A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.782A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.314A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.022A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.929A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.715A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 12.157A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 427 through 432 removed outlier: 3.586A pdb=" N ASN A 427 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 443 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 525 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 530 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 102 removed outlier: 3.767A pdb=" N GLU B 99 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 107 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 101 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 115 through 117 removed outlier: 3.649A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.538A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.676A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.886A pdb=" N ALA B 260 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 268 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 297 removed outlier: 6.889A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 345 through 346 removed outlier: 3.646A pdb=" N GLN B 360 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 31 through 35 removed outlier: 4.332A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN E 80 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 72 through 75 429 hydrogen bonds defined for protein. 1197 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: 3.48 Time building geometry restraints manager: 4.56 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: 3883 1.34 - 1.46: 2557 1.46 - 1.58: 5367 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 11869 Sorted by residual: bond pdb=" C SER B 198 " pdb=" N ALA B 199 " ideal model delta sigma weight residual 1.335 1.307 0.027 1.41e-02 5.03e+03 3.78e+00 bond pdb=" C LEU D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.34e+00 bond pdb=" CB VAL D 194 " pdb=" CG2 VAL D 194 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" N ARG B 77 " pdb=" CA ARG B 77 " ideal model delta sigma weight residual 1.461 1.478 -0.016 1.49e-02 4.50e+03 1.19e+00 bond pdb=" CA VAL B 147 " pdb=" CB VAL B 147 " ideal model delta sigma weight residual 1.542 1.559 -0.017 1.55e-02 4.16e+03 1.16e+00 ... (remaining 11864 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.28: 291 106.28 - 113.22: 6234 113.22 - 120.16: 4348 120.16 - 127.11: 5135 127.11 - 134.05: 125 Bond angle restraints: 16133 Sorted by residual: angle pdb=" N ALA B 78 " pdb=" CA ALA B 78 " pdb=" C ALA B 78 " ideal model delta sigma weight residual 114.75 108.00 6.75 1.26e+00 6.30e-01 2.87e+01 angle pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " pdb=" CG LEU A 450 " ideal model delta sigma weight residual 116.30 132.89 -16.59 3.50e+00 8.16e-02 2.25e+01 angle pdb=" C GLN E 52 " pdb=" N GLN E 53 " pdb=" CA GLN E 53 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 angle pdb=" CA LEU A 34 " pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " ideal model delta sigma weight residual 116.30 129.19 -12.89 3.50e+00 8.16e-02 1.36e+01 angle pdb=" N GLY A 443 " pdb=" CA GLY A 443 " pdb=" C GLY A 443 " ideal model delta sigma weight residual 110.96 115.24 -4.28 1.19e+00 7.06e-01 1.29e+01 ... (remaining 16128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6252 17.91 - 35.82: 626 35.82 - 53.74: 89 53.74 - 71.65: 24 71.65 - 89.56: 16 Dihedral angle restraints: 7007 sinusoidal: 2735 harmonic: 4272 Sorted by residual: dihedral pdb=" CB CYS A 435 " pdb=" SG CYS A 435 " pdb=" SG CYS A 665 " pdb=" CB CYS A 665 " ideal model delta sinusoidal sigma weight residual 93.00 14.17 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CA GLU B 39 " pdb=" C GLU B 39 " pdb=" N ASN B 40 " pdb=" CA ASN B 40 " ideal model delta harmonic sigma weight residual -180.00 -151.34 -28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ARG B 243 " pdb=" C ARG B 243 " pdb=" N LEU B 244 " pdb=" CA LEU B 244 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 7004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1226 0.049 - 0.098: 422 0.098 - 0.148: 105 0.148 - 0.197: 10 0.197 - 0.246: 2 Chirality restraints: 1765 Sorted by residual: chirality pdb=" CB VAL D 108 " pdb=" CA VAL D 108 " pdb=" CG1 VAL D 108 " pdb=" CG2 VAL D 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL C 76 " pdb=" N VAL C 76 " pdb=" C VAL C 76 " pdb=" CB VAL C 76 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE B 290 " pdb=" CA ILE B 290 " pdb=" CG1 ILE B 290 " pdb=" CG2 ILE B 290 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 1762 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 215 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO D 216 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 216 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 216 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 248 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO A 249 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 778 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 779 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 779 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 779 " -0.032 5.00e-02 4.00e+02 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3538 2.81 - 3.34: 9686 3.34 - 3.86: 18519 3.86 - 4.38: 19231 4.38 - 4.90: 34266 Nonbonded interactions: 85240 Sorted by model distance: nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.293 2.440 nonbonded pdb=" OG1 THR E 72 " pdb=" O LEU E 93 " model vdw 2.299 2.440 nonbonded pdb=" O LEU D 119 " pdb=" OG SER D 122 " model vdw 2.314 2.440 nonbonded pdb=" O ASN A 113 " pdb=" OG SER A 117 " model vdw 2.316 2.440 nonbonded pdb=" O GLU B 150 " pdb=" OG1 THR B 166 " model vdw 2.318 2.440 ... (remaining 85235 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 32 5.16 5 C 7323 2.51 5 N 1983 2.21 5 O 2279 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 6.550 Check model and map are aligned: 0.190 Process input model: 30.830 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 11869 Z= 0.314 Angle : 0.799 16.592 16133 Z= 0.445 Chirality : 0.052 0.246 1765 Planarity : 0.006 0.070 2123 Dihedral : 14.886 89.562 4288 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.18), residues: 1476 helix: -2.58 (0.20), residues: 286 sheet: -1.96 (0.23), residues: 430 loop : -2.90 (0.18), residues: 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 198 average time/residue: 0.2683 time to fit residues: 73.4892 Evaluate side-chains 125 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1145 time to fit residues: 2.6631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 297 ASN A 371 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN B 334 ASN B 336 ASN D 40 GLN D 41 GLN D 54 GLN D 60 ASN E 34 GLN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11869 Z= 0.291 Angle : 0.614 7.813 16133 Z= 0.327 Chirality : 0.044 0.146 1765 Planarity : 0.005 0.055 2123 Dihedral : 5.407 23.548 1628 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.20), residues: 1476 helix: -0.77 (0.27), residues: 295 sheet: -1.62 (0.25), residues: 416 loop : -2.67 (0.20), residues: 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 156 average time/residue: 0.2287 time to fit residues: 52.8489 Evaluate side-chains 111 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1034 time to fit residues: 2.1230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 170 GLN A 371 GLN A 441 GLN A 561 GLN A 666 ASN D 40 GLN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11869 Z= 0.242 Angle : 0.569 7.309 16133 Z= 0.299 Chirality : 0.043 0.155 1765 Planarity : 0.004 0.049 2123 Dihedral : 5.091 22.202 1628 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.21), residues: 1476 helix: 0.13 (0.30), residues: 294 sheet: -1.37 (0.24), residues: 430 loop : -2.44 (0.21), residues: 752 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.2139 time to fit residues: 49.6599 Evaluate side-chains 111 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1300 time to fit residues: 1.8782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 371 GLN A 666 ASN B 64 HIS D 116 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 11869 Z= 0.228 Angle : 0.555 7.315 16133 Z= 0.293 Chirality : 0.043 0.146 1765 Planarity : 0.004 0.048 2123 Dihedral : 4.931 22.027 1628 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.21), residues: 1476 helix: 0.36 (0.30), residues: 300 sheet: -1.22 (0.25), residues: 424 loop : -2.41 (0.21), residues: 752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.2149 time to fit residues: 46.9936 Evaluate side-chains 101 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN B 121 HIS ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 116 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 11869 Z= 0.306 Angle : 0.596 9.578 16133 Z= 0.313 Chirality : 0.044 0.156 1765 Planarity : 0.004 0.048 2123 Dihedral : 5.042 21.926 1628 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1476 helix: 0.53 (0.31), residues: 301 sheet: -1.18 (0.25), residues: 403 loop : -2.41 (0.21), residues: 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2230 time to fit residues: 48.2636 Evaluate side-chains 105 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 196 HIS A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN B 121 HIS D 54 GLN D 116 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 11869 Z= 0.163 Angle : 0.531 9.609 16133 Z= 0.277 Chirality : 0.043 0.164 1765 Planarity : 0.004 0.047 2123 Dihedral : 4.747 21.774 1628 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1476 helix: 0.62 (0.31), residues: 303 sheet: -1.06 (0.25), residues: 430 loop : -2.25 (0.22), residues: 743 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2293 time to fit residues: 51.0317 Evaluate side-chains 106 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 141 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 0.0050 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 139 HIS D 230 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 11869 Z= 0.135 Angle : 0.525 8.932 16133 Z= 0.275 Chirality : 0.043 0.163 1765 Planarity : 0.004 0.087 2123 Dihedral : 4.522 21.801 1628 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1476 helix: 0.63 (0.31), residues: 301 sheet: -0.83 (0.25), residues: 423 loop : -2.09 (0.22), residues: 752 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2441 time to fit residues: 58.1971 Evaluate side-chains 109 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 70 optimal weight: 0.0980 chunk 13 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 666 ASN B 121 HIS B 301 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11869 Z= 0.259 Angle : 0.578 8.517 16133 Z= 0.302 Chirality : 0.044 0.160 1765 Planarity : 0.004 0.066 2123 Dihedral : 4.685 21.249 1628 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1476 helix: 0.74 (0.31), residues: 302 sheet: -0.85 (0.25), residues: 422 loop : -2.09 (0.22), residues: 752 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2235 time to fit residues: 48.9211 Evaluate side-chains 106 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 0.0270 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 666 ASN B 121 HIS D 116 ASN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11869 Z= 0.165 Angle : 0.549 8.634 16133 Z= 0.283 Chirality : 0.043 0.154 1765 Planarity : 0.004 0.057 2123 Dihedral : 4.537 21.493 1628 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1476 helix: 0.87 (0.31), residues: 301 sheet: -0.73 (0.25), residues: 428 loop : -2.02 (0.22), residues: 747 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2307 time to fit residues: 51.3088 Evaluate side-chains 110 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1350 time to fit residues: 1.8599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 116 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN B 121 HIS D 116 ASN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11869 Z= 0.188 Angle : 0.564 8.381 16133 Z= 0.290 Chirality : 0.043 0.152 1765 Planarity : 0.004 0.054 2123 Dihedral : 4.535 21.376 1628 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.22), residues: 1476 helix: 0.86 (0.31), residues: 301 sheet: -0.71 (0.25), residues: 430 loop : -1.98 (0.22), residues: 745 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2273 time to fit residues: 50.4992 Evaluate side-chains 111 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 371 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN B 121 HIS D 116 ASN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077854 restraints weight = 28492.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080187 restraints weight = 16766.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081800 restraints weight = 11722.849| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11869 Z= 0.199 Angle : 0.562 8.297 16133 Z= 0.290 Chirality : 0.043 0.150 1765 Planarity : 0.004 0.047 2123 Dihedral : 4.583 21.323 1628 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1476 helix: 0.83 (0.31), residues: 306 sheet: -0.64 (0.26), residues: 412 loop : -1.98 (0.22), residues: 758 =============================================================================== Job complete usr+sys time: 2195.21 seconds wall clock time: 41 minutes 16.22 seconds (2476.22 seconds total)