Starting phenix.real_space_refine (version: dev) on Fri May 13 06:01:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/05_2022/7tyf_26178_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/05_2022/7tyf_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_26178/05_2022/7tyf_26178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/05_2022/7tyf_26178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/05_2022/7tyf_26178_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyf_26178/05_2022/7tyf_26178_updated.pdb" } resolution = 2.2 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= -0.000 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 Convert atoms to be neutral 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-dev-4597/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: {'undetermined': 1, 'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33, 'NH2_CTERM': 1} Conformer: "B" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1, 'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33, 'NH2_CTERM': 1} 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: {'PLM': 9, 'Y01': 2, 'NAG': 2, 'PTY': 1, 'P42': 1} Classifications: {'undetermined': 15, 'peptide': 367} 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: 54 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: 6.51, per 1000 atoms: 0.63 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: 4.64 Conformation dependent library (CDL) restraints added in 1.5 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... running ksdssp... Secondary structure from input PDB file: 37 helices and 11 sheets defined 40.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.564A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 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 371 through 390 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'E' and resid 34 through 47 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 61 through 80 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 87 through 99 Processing helix chain 'E' and resid 116 through 142 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 5 through 18 removed outlier: 4.848A pdb=" N THR P 9 " --> pdb=" O THR P 6 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA P 13 " --> pdb=" O GLN P 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN P 14 " --> pdb=" O ARG P 11 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL P 17 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 61 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) Processing helix chain 'R' and resid 132 through 136 Processing helix chain 'R' and resid 138 through 172 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 176 No H-bonds generated for 'chain 'R' and resid 174 through 176' Processing helix chain 'R' and resid 179 through 203 Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 217 through 248 Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 269 through 283 Proline residue: R 273 - end of helix removed outlier: 3.785A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 296 through 329 removed outlier: 3.847A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.502A pdb=" N VAL R 311 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 320 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 324 " --> pdb=" O ARG R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 352 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 358 removed outlier: 3.687A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 381 Processing helix chain 'R' and resid 383 through 391 Processing helix chain 'R' and resid 396 through 408 removed outlier: 4.665A pdb=" N ALA R 407 " --> pdb=" O LYS R 403 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.133A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, 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= C, 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= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.707A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (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= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.928A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.633A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.399A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (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= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.478A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, 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= K, first strand: chain 'R' and resid 90 through 94 453 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 4.92 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=" 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 bond pdb=" N SER E 103 " pdb=" CA SER E 103 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.15e+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: 5936 26.66 - 53.32: 231 53.32 - 79.98: 44 79.98 - 106.64: 2 106.64 - 133.30: 2 Dihedral angle restraints: 6215 sinusoidal: 2523 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 6212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1142 0.041 - 0.082: 312 0.082 - 0.123: 95 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: 1835 2.77 - 3.30: 10037 3.30 - 3.83: 18052 3.83 - 4.37: 22382 4.37 - 4.90: 36269 Nonbonded interactions: 88575 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 88570 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: 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. 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: 0.900 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: 6.210 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.100 Process input model: 30.630 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.004 0.050 10479 Z= 0.249 Angle : 0.568 9.523 14168 Z= 0.324 Chirality : 0.042 0.204 1558 Planarity : 0.003 0.034 1776 Dihedral : 14.435 133.305 3804 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.87 % 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 *********************** 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 : 1.140 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 193 average time/residue: 1.3898 time to fit residues: 286.1952 Evaluate side-chains 167 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.5918 ------------------------------------------------------------------------------- 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: 7.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 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 32 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8250 moved from start: 0.1325 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= 0.245 Angle : 0.607 7.358 14168 Z= 0.328 Chirality : 0.046 0.362 1558 Planarity : 0.005 0.040 1776 Dihedral : 8.181 98.755 1611 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 3.00 % 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: -0.24 (0.22), residues: 1251 helix: 0.65 (0.22), residues: 500 sheet: -0.01 (0.33), residues: 227 loop : -0.94 (0.25), residues: 524 *********************** 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 207 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.237 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 192 average time/residue: 1.2840 time to fit residues: 264.9950 Evaluate side-chains 174 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.4007 time to fit residues: 3.9982 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 3 GLN N 13 GLN N 77 ASN R 201 HIS R 365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10479 Z= 0.157 Angle : 0.521 7.712 14168 Z= 0.278 Chirality : 0.042 0.146 1558 Planarity : 0.004 0.041 1776 Dihedral : 7.256 75.589 1611 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.42 % 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: 0.22 (0.23), residues: 1251 helix: 1.11 (0.23), residues: 511 sheet: 0.07 (0.33), residues: 224 loop : -0.72 (0.27), residues: 516 *********************** 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 196 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 184 average time/residue: 1.3491 time to fit residues: 265.7125 Evaluate side-chains 174 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.7510 time to fit residues: 3.3246 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 3 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10479 Z= 0.190 Angle : 0.552 7.844 14168 Z= 0.294 Chirality : 0.043 0.151 1558 Planarity : 0.004 0.041 1776 Dihedral : 7.510 77.478 1611 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 2.52 % 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: 0.33 (0.24), residues: 1251 helix: 1.20 (0.23), residues: 511 sheet: 0.06 (0.33), residues: 228 loop : -0.63 (0.27), residues: 512 *********************** 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 192 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.102 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 1.3113 time to fit residues: 252.8086 Evaluate side-chains 179 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.3263 time to fit residues: 4.0185 ------------------------------------------------------------------------------- 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: 6.9990 chunk 68 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 3 GLN R 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 10479 Z= 0.156 Angle : 0.519 8.105 14168 Z= 0.275 Chirality : 0.041 0.148 1558 Planarity : 0.004 0.041 1776 Dihedral : 7.263 76.717 1611 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 2.61 % 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: 0.48 (0.24), residues: 1251 helix: 1.32 (0.23), residues: 511 sheet: 0.27 (0.33), residues: 228 loop : -0.63 (0.27), residues: 512 *********************** 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 193 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 185 average time/residue: 1.3118 time to fit residues: 259.9346 Evaluate side-chains 178 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1326 time to fit residues: 2.4422 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 16 ASN B 340 ASN N 35 ASN ** 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: 0.8260 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 10479 Z= 0.290 Angle : 0.645 8.019 14168 Z= 0.343 Chirality : 0.047 0.185 1558 Planarity : 0.005 0.041 1776 Dihedral : 8.589 82.540 1611 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.61 % 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: 0.26 (0.23), residues: 1251 helix: 1.14 (0.23), residues: 503 sheet: 0.14 (0.32), residues: 237 loop : -0.71 (0.27), residues: 511 *********************** 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 196 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.226 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 184 average time/residue: 1.3256 time to fit residues: 261.7231 Evaluate side-chains 184 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.2997 time to fit residues: 4.3858 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 overall best weight: 1.1780 ------------------------------------------------------------------------------- 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 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10479 Z= 0.167 Angle : 0.565 13.771 14168 Z= 0.296 Chirality : 0.042 0.148 1558 Planarity : 0.004 0.040 1776 Dihedral : 7.838 81.569 1611 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 2.03 % 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: 0.47 (0.24), residues: 1251 helix: 1.33 (0.23), residues: 512 sheet: 0.30 (0.33), residues: 228 loop : -0.67 (0.27), residues: 511 *********************** 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 189 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 184 average time/residue: 1.3857 time to fit residues: 272.9116 Evaluate side-chains 176 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 2 average time/residue: 0.8810 time to fit residues: 3.5117 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 11 optimal weight: 0.2980 chunk 93 optimal weight: 30.0000 chunk 108 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 16 ASN B 91 HIS B 340 ASN N 13 GLN N 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 10479 Z= 0.135 Angle : 0.543 14.826 14168 Z= 0.280 Chirality : 0.040 0.138 1558 Planarity : 0.004 0.040 1776 Dihedral : 7.186 78.246 1611 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 2.13 % 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: 0.71 (0.24), residues: 1251 helix: 1.57 (0.24), residues: 513 sheet: 0.37 (0.33), residues: 228 loop : -0.57 (0.28), residues: 510 *********************** 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 199 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 196 average time/residue: 1.3356 time to fit residues: 280.4061 Evaluate side-chains 182 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0924 time to fit residues: 1.8523 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 N 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 10479 Z= 0.146 Angle : 0.547 14.211 14168 Z= 0.283 Chirality : 0.041 0.137 1558 Planarity : 0.004 0.040 1776 Dihedral : 7.232 78.928 1611 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.84 % 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: 0.72 (0.24), residues: 1251 helix: 1.58 (0.24), residues: 513 sheet: 0.34 (0.33), residues: 228 loop : -0.55 (0.28), residues: 510 *********************** 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 190 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 186 average time/residue: 1.3509 time to fit residues: 268.9371 Evaluate side-chains 185 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.4375 time to fit residues: 3.1842 ------------------------------------------------------------------------------- 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: 4.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 N 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10479 Z= 0.180 Angle : 0.590 13.456 14168 Z= 0.307 Chirality : 0.051 1.101 1558 Planarity : 0.004 0.041 1776 Dihedral : 7.606 81.307 1611 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.55 % 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: 0.67 (0.24), residues: 1251 helix: 1.55 (0.24), residues: 512 sheet: 0.28 (0.33), residues: 230 loop : -0.56 (0.28), residues: 509 ********************** 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 189 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 187 average time/residue: 1.4037 time to fit residues: 282.7906 Evaluate side-chains 183 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.6031 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.0030 chunk 86 optimal weight: 20.0000 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149563 restraints weight = 17235.653| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 4.05 r_work: 0.3412 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work: 0.3245 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10479 Z= 0.145 Angle : 0.563 12.746 14168 Z= 0.290 Chirality : 0.046 0.797 1558 Planarity : 0.004 0.040 1776 Dihedral : 7.282 80.927 1611 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 1.36 % 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: 0.75 (0.24), residues: 1251 helix: 1.61 (0.24), residues: 513 sheet: 0.29 (0.33), residues: 228 loop : -0.50 (0.28), residues: 510 =============================================================================== Job complete usr+sys time: 4295.10 seconds wall clock time: 76 minutes 40.50 seconds (4600.50 seconds total)