Starting phenix.real_space_refine on Sat Dec 9 06:41:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/12_2023/7tyf_26178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/12_2023/7tyf_26178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/12_2023/7tyf_26178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/12_2023/7tyf_26178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/12_2023/7tyf_26178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/12_2023/7tyf_26178.pdb" } resolution = 2.2 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= -0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 71 5.16 5 C 6599 2.51 5 N 1730 2.21 5 O 1929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10331 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1857 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 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: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 759 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 105} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Conformer: "B" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 266 Chain: "R" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3344 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 9, 'PTY': 1, 'Y01': 2} Classifications: {'peptide': 367, 'undetermined': 15} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 350, None: 15} Not linked: pdbres="PHE R 409 " pdbres="NAG R 501 " Not linked: pdbres="NAG R 501 " pdbres="NAG R 502 " Not linked: pdbres="NAG R 502 " pdbres="PLM R 503 " Not linked: pdbres="PLM R 503 " pdbres="PLM R 504 " Not linked: pdbres="PLM R 504 " pdbres="Y01 R 505 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG P 18 " occ=0.50 Time building chain proxies: 6.21, per 1000 atoms: 0.60 Number of scatterers: 10331 At special positions: 0 Unit cell: (109.56, 98.77, 151.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 2 15.00 O 1929 8.00 N 1730 7.00 C 6599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.04 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 45.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.564A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.945A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.533A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.830A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.627A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 34 through 48 removed outlier: 4.338A pdb=" N CYS E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 81 removed outlier: 3.748A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 143 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix removed outlier: 3.509A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.500A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 44 through 62 removed outlier: 3.628A pdb=" N MET R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 62 " --> pdb=" O ARG R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 137 removed outlier: 4.512A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.547A pdb=" N ASN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.577A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.689A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'R' and resid 406 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.464A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.875A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.746A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.685A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.639A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.537A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.707A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.114A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.562A pdb=" N CYS R 72 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 528 hydrogen bonds defined for protein. 1489 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: 3.14 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1692 1.32 - 1.45: 2895 1.45 - 1.58: 5789 1.58 - 1.70: 4 1.70 - 1.83: 99 Bond restraints: 10479 Sorted by residual: bond pdb=" C TYR P 37 " pdb=" N NH2 P 38 " ideal model delta sigma weight residual 2.329 1.324 1.005 1.40e-02 5.10e+03 5.15e+03 bond pdb=" N ILE E 106 " pdb=" CA ILE E 106 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 8.20e+00 bond pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 6.95e+00 bond pdb=" N THR E 54 " pdb=" CA THR E 54 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.53e+00 bond pdb=" OBN P42 R 510 " pdb=" PBM P42 R 510 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.36e+00 ... (remaining 10474 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.97: 201 105.97 - 113.03: 5540 113.03 - 120.09: 3744 120.09 - 127.16: 4549 127.16 - 134.22: 134 Bond angle restraints: 14168 Sorted by residual: angle pdb=" N ILE E 118 " pdb=" CA ILE E 118 " pdb=" C ILE E 118 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 111.81 109.07 2.74 8.60e-01 1.35e+00 1.02e+01 angle pdb=" O11 PTY R 514 " pdb=" P1 PTY R 514 " pdb=" O14 PTY R 514 " ideal model delta sigma weight residual 92.90 102.42 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N THR E 54 " pdb=" CA THR E 54 " pdb=" C THR E 54 " ideal model delta sigma weight residual 113.16 109.37 3.79 1.24e+00 6.50e-01 9.34e+00 angle pdb=" CA LEU E 55 " pdb=" C LEU E 55 " pdb=" O LEU E 55 " ideal model delta sigma weight residual 120.55 117.60 2.95 1.06e+00 8.90e-01 7.72e+00 ... (remaining 14163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.66: 6089 26.66 - 53.32: 241 53.32 - 79.98: 48 79.98 - 106.64: 4 106.64 - 133.30: 2 Dihedral angle restraints: 6384 sinusoidal: 2692 harmonic: 3692 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual -86.00 -21.95 -64.05 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual 93.00 147.10 -54.10 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1140 0.041 - 0.082: 313 0.082 - 0.123: 96 0.123 - 0.164: 6 0.164 - 0.204: 3 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CBE P42 R 510 " pdb=" CAB P42 R 510 " pdb=" CBK P42 R 510 " pdb=" OBD P42 R 510 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE E 106 " pdb=" N ILE E 106 " pdb=" C ILE E 106 " pdb=" CB ILE E 106 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" C1 NAG R 502 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 502 " pdb=" O5 NAG R 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 1555 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 73 " -0.016 2.00e-02 2.50e+03 1.48e-02 2.72e+00 pdb=" CG ASN R 73 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN R 73 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN R 73 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG R 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO B 236 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.84e+00 pdb=" N PRO R 304 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.019 5.00e-02 4.00e+02 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1828 2.77 - 3.30: 9967 3.30 - 3.83: 18014 3.83 - 4.37: 22208 4.37 - 4.90: 36257 Nonbonded interactions: 88274 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.234 2.440 nonbonded pdb=" O LEU P 16 " pdb=" OG SER P 20 " model vdw 2.274 2.440 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.292 2.520 nonbonded pdb=" OD1 ASP N 106 " pdb=" O HOH N 201 " model vdw 2.294 2.440 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.300 2.520 ... (remaining 88269 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=0.50 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: 5.760 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.270 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.011 1.005 10479 Z= 0.856 Angle : 0.572 9.523 14168 Z= 0.324 Chirality : 0.042 0.204 1558 Planarity : 0.003 0.034 1776 Dihedral : 14.565 133.305 3973 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.87 % Allowed : 10.84 % Favored : 88.29 % 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: -1.73 (0.20), residues: 1251 helix: -1.23 (0.18), residues: 503 sheet: -0.21 (0.32), residues: 226 loop : -1.32 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 65 ARG 0.004 0.000 ARG R 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.104 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 193 average time/residue: 1.5012 time to fit residues: 307.4960 Evaluate side-chains 167 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.5591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 294 GLN B 16 ASN B 75 GLN B 88 ASN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 13 GLN N 77 ASN P 22 ASN R 144 ASN R 201 HIS R 318 ASN R 365 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10479 Z= 0.248 Angle : 0.623 7.488 14168 Z= 0.336 Chirality : 0.046 0.278 1558 Planarity : 0.005 0.040 1776 Dihedral : 8.993 102.738 1780 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.90 % Allowed : 12.29 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1251 helix: 0.97 (0.22), residues: 508 sheet: -0.14 (0.32), residues: 239 loop : -1.00 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.007 0.001 HIS A 41 PHE 0.015 0.002 PHE B 151 TYR 0.021 0.002 TYR R 56 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.171 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 196 average time/residue: 1.3566 time to fit residues: 283.7656 Evaluate side-chains 176 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.4346 time to fit residues: 3.6745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 13 GLN N 77 ASN R 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10479 Z= 0.147 Angle : 0.521 7.751 14168 Z= 0.278 Chirality : 0.042 0.161 1558 Planarity : 0.004 0.041 1776 Dihedral : 7.982 74.432 1780 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.52 % Allowed : 13.75 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1251 helix: 1.72 (0.23), residues: 512 sheet: -0.05 (0.33), residues: 238 loop : -0.78 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.001 PHE B 151 TYR 0.020 0.001 TYR R 56 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.177 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 190 average time/residue: 1.4240 time to fit residues: 288.1681 Evaluate side-chains 177 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.6725 time to fit residues: 3.0526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN N 3 GLN N 13 GLN ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10479 Z= 0.278 Angle : 0.652 8.761 14168 Z= 0.346 Chirality : 0.053 0.955 1558 Planarity : 0.005 0.043 1776 Dihedral : 8.993 77.543 1780 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.00 % Allowed : 14.42 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1251 helix: 1.62 (0.23), residues: 505 sheet: -0.09 (0.32), residues: 243 loop : -0.77 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 234 HIS 0.008 0.002 HIS A 41 PHE 0.016 0.002 PHE R 269 TYR 0.019 0.002 TYR R 56 ARG 0.007 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.164 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 188 average time/residue: 1.3588 time to fit residues: 272.8930 Evaluate side-chains 182 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.3927 time to fit residues: 3.3327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10479 Z= 0.209 Angle : 0.592 8.157 14168 Z= 0.315 Chirality : 0.048 0.715 1558 Planarity : 0.004 0.040 1776 Dihedral : 8.737 77.974 1780 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.19 % Allowed : 14.62 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1251 helix: 1.81 (0.23), residues: 506 sheet: 0.03 (0.32), residues: 237 loop : -0.79 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.002 TYR R 56 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.141 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 191 average time/residue: 1.3979 time to fit residues: 284.7903 Evaluate side-chains 188 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 7 average time/residue: 0.2704 time to fit residues: 4.0085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 40.0000 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 35 GLN B 16 ASN N 3 GLN R 125 ASN ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10479 Z= 0.380 Angle : 0.747 8.010 14168 Z= 0.398 Chirality : 0.054 0.663 1558 Planarity : 0.005 0.040 1776 Dihedral : 10.358 88.215 1780 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.39 % Allowed : 14.33 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1251 helix: 1.37 (0.22), residues: 505 sheet: 0.02 (0.31), residues: 248 loop : -0.86 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 234 HIS 0.010 0.002 HIS A 41 PHE 0.020 0.003 PHE R 269 TYR 0.017 0.003 TYR A 358 ARG 0.011 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.062 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 185 average time/residue: 1.3526 time to fit residues: 267.3992 Evaluate side-chains 187 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.6494 time to fit residues: 6.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 340 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10479 Z= 0.169 Angle : 0.563 8.434 14168 Z= 0.298 Chirality : 0.045 0.576 1558 Planarity : 0.004 0.040 1776 Dihedral : 9.149 84.391 1780 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.61 % Allowed : 15.88 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1251 helix: 1.92 (0.23), residues: 509 sheet: 0.15 (0.32), residues: 241 loop : -0.76 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.015 0.001 PHE B 151 TYR 0.013 0.001 TYR P 37 ARG 0.006 0.000 ARG R 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 188 average time/residue: 1.4290 time to fit residues: 286.0861 Evaluate side-chains 186 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1561 time to fit residues: 2.5483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS B 340 ASN N 3 GLN ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10479 Z= 0.341 Angle : 0.716 8.763 14168 Z= 0.380 Chirality : 0.051 0.581 1558 Planarity : 0.005 0.041 1776 Dihedral : 10.075 87.993 1780 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.32 % Allowed : 15.78 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1251 helix: 1.61 (0.23), residues: 506 sheet: 0.04 (0.31), residues: 255 loop : -0.79 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 234 HIS 0.009 0.002 HIS A 41 PHE 0.019 0.002 PHE R 269 TYR 0.017 0.003 TYR A 358 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.134 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 183 average time/residue: 1.4481 time to fit residues: 282.1675 Evaluate side-chains 182 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.2359 time to fit residues: 1.8744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10479 Z= 0.153 Angle : 0.553 9.044 14168 Z= 0.290 Chirality : 0.044 0.523 1558 Planarity : 0.004 0.039 1776 Dihedral : 8.920 87.708 1780 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.84 % Allowed : 16.26 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1251 helix: 2.01 (0.23), residues: 515 sheet: 0.17 (0.32), residues: 241 loop : -0.72 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.001 TYR R 56 ARG 0.006 0.000 ARG R 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 191 average time/residue: 1.4161 time to fit residues: 288.4060 Evaluate side-chains 178 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.0994 time to fit residues: 1.9268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.0020 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 16 ASN B 340 ASN N 13 GLN R 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10479 Z= 0.144 Angle : 0.538 9.149 14168 Z= 0.281 Chirality : 0.043 0.499 1558 Planarity : 0.004 0.039 1776 Dihedral : 8.391 86.192 1780 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.74 % Allowed : 16.65 % Favored : 81.61 % 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: 1.07 (0.24), residues: 1251 helix: 2.29 (0.23), residues: 509 sheet: 0.19 (0.32), residues: 241 loop : -0.67 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.002 0.001 HIS R 302 PHE 0.012 0.001 PHE R 161 TYR 0.016 0.001 TYR R 56 ARG 0.006 0.000 ARG R 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 191 average time/residue: 1.4250 time to fit residues: 292.1513 Evaluate side-chains 180 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1458 time to fit residues: 1.6728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 340 ASN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.193514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.146394 restraints weight = 17134.587| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.07 r_work: 0.3076 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10479 Z= 0.200 Angle : 0.599 9.051 14168 Z= 0.314 Chirality : 0.045 0.490 1558 Planarity : 0.004 0.040 1776 Dihedral : 8.807 89.794 1780 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 16.94 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1251 helix: 2.11 (0.23), residues: 516 sheet: 0.18 (0.32), residues: 241 loop : -0.72 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.002 TYR R 56 ARG 0.004 0.000 ARG R 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4848.35 seconds wall clock time: 86 minutes 10.49 seconds (5170.49 seconds total)