Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:39:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fig_31596/04_2023/7fig_31596_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fig_31596/04_2023/7fig_31596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fig_31596/04_2023/7fig_31596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fig_31596/04_2023/7fig_31596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fig_31596/04_2023/7fig_31596_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fig_31596/04_2023/7fig_31596_neut.pdb" } resolution = 3.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1474 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 8122 2.51 5 N 2214 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12839 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2932 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 350} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: "R" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4334 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "X" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 678 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "Y" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.98, per 1000 atoms: 0.54 Number of scatterers: 12839 At special positions: 0 Unit cell: (93.005, 97.185, 182.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2404 8.00 N 2214 7.00 C 8122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.06 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 156 " distance=2.03 Simple disulfide: pdb=" SG CYS R 279 " - pdb=" SG CYS R 343 " distance=2.03 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 353 " distance=2.02 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.02 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R2000 " - " ASN R 174 " " NAG R2001 " - " ASN R 195 " " NAG X 101 " - " ASN X 52 " " NAG X 102 " - " ASN X 78 " " NAG Y1000 " - " ASN Y 13 " Time building additional restraints: 5.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3082 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 36.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.514A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 91 Processing helix chain 'A' and resid 99 through 113 removed outlier: 4.087A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.826A pdb=" N ALA A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.691A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.613A pdb=" N TYR A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.690A pdb=" N VAL A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.471A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.115A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 4.152A pdb=" N ARG A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.575A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.589A pdb=" N PHE R 145 " --> pdb=" O THR R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 219 Processing helix chain 'R' and resid 241 through 245 Processing helix chain 'R' and resid 261 through 266 removed outlier: 3.747A pdb=" N VAL R 266 " --> pdb=" O GLU R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 283 removed outlier: 3.882A pdb=" N PHE R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 337 removed outlier: 3.918A pdb=" N LEU R 337 " --> pdb=" O GLY R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 387 removed outlier: 3.595A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 423 Processing helix chain 'R' and resid 425 through 436 removed outlier: 3.815A pdb=" N HIS R 429 " --> pdb=" O GLN R 425 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 Processing helix chain 'R' and resid 479 through 500 Processing helix chain 'R' and resid 507 through 511 removed outlier: 3.953A pdb=" N VAL R 511 " --> pdb=" O TYR R 508 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 560 through 594 removed outlier: 3.988A pdb=" N ALA R 568 " --> pdb=" O ASP R 564 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE R 573 " --> pdb=" O LYS R 569 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 574 " --> pdb=" O LYS R 570 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP R 578 " --> pdb=" O LEU R 574 " (cutoff:3.500A) Proline residue: R 584 - end of helix removed outlier: 3.590A pdb=" N SER R 591 " --> pdb=" O PHE R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 603 through 623 removed outlier: 3.777A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Proline residue: R 613 - end of helix removed outlier: 4.600A pdb=" N SER R 616 " --> pdb=" O TYR R 612 " (cutoff:3.500A) Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 641 removed outlier: 3.749A pdb=" N ASP R 633 " --> pdb=" O THR R 629 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.956A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 50 removed outlier: 3.566A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.781A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.826A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.405A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.911A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.660A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.803A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.745A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 53 through 56 removed outlier: 6.002A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR R 133 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN R 107 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN R 195 " --> pdb=" O GLY R 220 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR R 222 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR R 197 " --> pdb=" O THR R 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 53 through 56 removed outlier: 6.002A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR R 133 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN R 107 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N THR R 226 " --> pdb=" O THR R 198 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR R 200 " --> pdb=" O THR R 226 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP R 228 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU R 202 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU R 227 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 63 through 64 Processing sheet with id=AB6, first strand: chain 'R' and resid 94 through 95 removed outlier: 6.348A pdb=" N PHE R 94 " --> pdb=" O ILE R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'R' and resid 163 through 164 removed outlier: 3.502A pdb=" N VAL R 189 " --> pdb=" O LYS R 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 11 through 14 removed outlier: 10.790A pdb=" N THR Y 32 " --> pdb=" O PRO X 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AC1, first strand: chain 'X' and resid 59 through 69 removed outlier: 5.956A pdb=" N CYS X 60 " --> pdb=" O CYS X 84 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N CYS X 84 " --> pdb=" O CYS X 60 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA X 62 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS X 82 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER X 64 " --> pdb=" O THR X 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 91 through 92 Processing sheet with id=AC3, first strand: chain 'Y' and resid 56 through 68 removed outlier: 6.544A pdb=" N SER Y 87 " --> pdb=" O ARG Y 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL Y 62 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA Y 85 " --> pdb=" O VAL Y 62 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE Y 64 " --> pdb=" O ALA Y 83 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA Y 83 " --> pdb=" O PHE Y 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER Y 66 " --> pdb=" O SER Y 81 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER Y 81 " --> pdb=" O SER Y 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG Y 68 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL Y 79 " --> pdb=" O ARG Y 68 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1599 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: 4.43 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2509 1.33 - 1.45: 3171 1.45 - 1.57: 7282 1.57 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13096 Sorted by residual: bond pdb=" CZ ARG A 205 " pdb=" NH2 ARG A 205 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 90 " pdb=" NH2 ARG A 90 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 144 " pdb=" NH2 ARG A 144 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" CZ ARG A 142 " pdb=" NH2 ARG A 142 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" CZ ARG N 98 " pdb=" NH2 ARG N 98 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 13091 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.52: 371 106.52 - 113.63: 7095 113.63 - 120.74: 5802 120.74 - 127.84: 4363 127.84 - 134.95: 120 Bond angle restraints: 17751 Sorted by residual: angle pdb=" CA ASP N 50 " pdb=" CB ASP N 50 " pdb=" CG ASP N 50 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 angle pdb=" C ARG N 105 " pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 120.65 129.03 -8.38 1.32e+00 5.74e-01 4.03e+01 angle pdb=" CA PHE N 68 " pdb=" CB PHE N 68 " pdb=" CG PHE N 68 " ideal model delta sigma weight residual 113.80 119.65 -5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.00e+00 1.00e+00 3.36e+01 angle pdb=" C GLN B 176 " pdb=" N THR B 177 " pdb=" CA THR B 177 " ideal model delta sigma weight residual 120.63 129.34 -8.71 1.61e+00 3.86e-01 2.93e+01 ... (remaining 17746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7239 17.46 - 34.93: 543 34.93 - 52.39: 74 52.39 - 69.85: 26 69.85 - 87.31: 16 Dihedral angle restraints: 7898 sinusoidal: 3133 harmonic: 4765 Sorted by residual: dihedral pdb=" CA CYS B 204 " pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 7895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1723 0.076 - 0.152: 250 0.152 - 0.228: 51 0.228 - 0.305: 10 0.305 - 0.381: 4 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CA TYR A 69 " pdb=" N TYR A 69 " pdb=" C TYR A 69 " pdb=" CB TYR A 69 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA THR N 114 " pdb=" N THR N 114 " pdb=" C THR N 114 " pdb=" CB THR N 114 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA CYS N 107 " pdb=" N CYS N 107 " pdb=" C CYS N 107 " pdb=" CB CYS N 107 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 2035 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 95 " 0.146 2.00e-02 2.50e+03 8.22e-02 1.35e+02 pdb=" CG TYR N 95 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR N 95 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR N 95 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR N 95 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR N 95 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR N 95 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR N 95 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 167 " 0.116 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" CG TYR A 167 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 167 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 167 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 167 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 167 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 167 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 167 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 154 " -0.121 2.00e-02 2.50e+03 6.31e-02 7.96e+01 pdb=" CG TYR A 154 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 154 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR A 154 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 154 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 154 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 154 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 154 " -0.085 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 116 2.59 - 3.17: 11968 3.17 - 3.74: 20140 3.74 - 4.32: 28900 4.32 - 4.90: 47044 Nonbonded interactions: 108168 Sorted by model distance: nonbonded pdb=" O CYS B 204 " pdb=" OD1 ASP B 228 " model vdw 2.011 3.040 nonbonded pdb=" NZ LYS B 57 " pdb=" OE1 GLN B 75 " model vdw 2.028 2.520 nonbonded pdb=" O3 NAG Y1000 " pdb=" O7 NAG Y1000 " model vdw 2.166 2.440 nonbonded pdb=" NE2 GLN R 170 " pdb=" O6 NAG R2001 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG B 48 " pdb=" OD1 ASN B 340 " model vdw 2.267 2.520 ... (remaining 108163 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.900 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.510 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.007 0.048 13096 Z= 0.458 Angle : 1.106 8.711 17751 Z= 0.720 Chirality : 0.061 0.381 2038 Planarity : 0.012 0.172 2270 Dihedral : 13.421 87.313 4765 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.19), residues: 1616 helix: -1.57 (0.18), residues: 513 sheet: -1.25 (0.28), residues: 327 loop : -1.12 (0.21), residues: 776 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.2583 time to fit residues: 181.2421 Evaluate side-chains 301 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 81 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN G 44 HIS N 35 ASN R 160 HIS R 170 GLN ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13096 Z= 0.223 Angle : 0.758 8.608 17751 Z= 0.390 Chirality : 0.046 0.192 2038 Planarity : 0.005 0.037 2270 Dihedral : 6.644 56.576 1779 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.65 (0.21), residues: 1616 helix: 0.30 (0.22), residues: 503 sheet: -1.26 (0.27), residues: 335 loop : -0.38 (0.23), residues: 778 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 375 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 399 average time/residue: 0.2419 time to fit residues: 140.5779 Evaluate side-chains 315 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 287 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1212 time to fit residues: 8.2567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 141 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 91 HIS B 110 ASN N 123 GLN R 96 ASN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN X 83 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 13096 Z= 0.327 Angle : 0.734 9.328 17751 Z= 0.382 Chirality : 0.046 0.179 2038 Planarity : 0.004 0.036 2270 Dihedral : 6.309 55.362 1779 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.53 (0.21), residues: 1616 helix: 0.40 (0.23), residues: 516 sheet: -1.21 (0.28), residues: 330 loop : -0.31 (0.23), residues: 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 297 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 34 residues processed: 329 average time/residue: 0.2437 time to fit residues: 117.5392 Evaluate side-chains 290 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1259 time to fit residues: 10.0784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 619 ASN X 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 13096 Z= 0.244 Angle : 0.699 10.111 17751 Z= 0.359 Chirality : 0.045 0.178 2038 Planarity : 0.004 0.036 2270 Dihedral : 5.985 53.932 1779 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.39 (0.21), residues: 1616 helix: 0.52 (0.23), residues: 509 sheet: -1.03 (0.27), residues: 343 loop : -0.27 (0.24), residues: 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 293 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 317 average time/residue: 0.2510 time to fit residues: 115.4058 Evaluate side-chains 280 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1432 time to fit residues: 7.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN R 425 GLN X 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 13096 Z= 0.251 Angle : 0.707 13.445 17751 Z= 0.359 Chirality : 0.045 0.195 2038 Planarity : 0.004 0.038 2270 Dihedral : 5.833 52.231 1779 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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 (0.21), residues: 1616 helix: 0.57 (0.23), residues: 504 sheet: -0.96 (0.27), residues: 342 loop : -0.22 (0.24), residues: 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 298 average time/residue: 0.2558 time to fit residues: 111.3216 Evaluate side-chains 277 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 260 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1262 time to fit residues: 6.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 127 optimal weight: 0.0000 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN X 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 13096 Z= 0.260 Angle : 0.738 13.839 17751 Z= 0.375 Chirality : 0.045 0.273 2038 Planarity : 0.004 0.042 2270 Dihedral : 5.783 51.792 1779 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.27 (0.21), residues: 1616 helix: 0.61 (0.23), residues: 514 sheet: -0.89 (0.27), residues: 342 loop : -0.23 (0.24), residues: 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 293 average time/residue: 0.2443 time to fit residues: 105.1704 Evaluate side-chains 269 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 253 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1220 time to fit residues: 5.6403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 142 HIS ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 31 ASN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 13096 Z= 0.219 Angle : 0.731 16.057 17751 Z= 0.370 Chirality : 0.044 0.229 2038 Planarity : 0.004 0.040 2270 Dihedral : 5.625 49.971 1779 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1616 helix: 0.67 (0.23), residues: 513 sheet: -0.82 (0.27), residues: 344 loop : -0.34 (0.24), residues: 759 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 289 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 300 average time/residue: 0.2541 time to fit residues: 111.2158 Evaluate side-chains 271 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 259 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1293 time to fit residues: 4.9811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.0970 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13096 Z= 0.211 Angle : 0.761 15.475 17751 Z= 0.383 Chirality : 0.045 0.209 2038 Planarity : 0.004 0.041 2270 Dihedral : 5.587 48.351 1779 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.23 (0.21), residues: 1616 helix: 0.68 (0.23), residues: 514 sheet: -0.86 (0.27), residues: 362 loop : -0.22 (0.24), residues: 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 279 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 286 average time/residue: 0.2616 time to fit residues: 109.7840 Evaluate side-chains 272 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1372 time to fit residues: 5.5155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 85 optimal weight: 0.0370 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 0.0980 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 142 HIS G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 GLN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 13096 Z= 0.206 Angle : 0.763 13.430 17751 Z= 0.382 Chirality : 0.045 0.201 2038 Planarity : 0.004 0.042 2270 Dihedral : 5.504 55.912 1779 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.27 (0.22), residues: 1616 helix: 0.70 (0.23), residues: 508 sheet: -0.96 (0.26), residues: 377 loop : -0.20 (0.25), residues: 731 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 279 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 287 average time/residue: 0.2542 time to fit residues: 106.3865 Evaluate side-chains 267 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1199 time to fit residues: 2.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 13096 Z= 0.332 Angle : 0.829 16.062 17751 Z= 0.418 Chirality : 0.047 0.217 2038 Planarity : 0.005 0.041 2270 Dihedral : 5.716 55.974 1779 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.40 (0.21), residues: 1616 helix: 0.53 (0.23), residues: 512 sheet: -1.03 (0.27), residues: 358 loop : -0.28 (0.24), residues: 746 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 275 average time/residue: 0.2393 time to fit residues: 97.9215 Evaluate side-chains 262 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 251 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1284 time to fit residues: 4.8461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 311 HIS G 18 GLN N 123 GLN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.130798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095131 restraints weight = 27477.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098954 restraints weight = 13929.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101458 restraints weight = 9229.821| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 13096 Z= 0.210 Angle : 0.791 15.891 17751 Z= 0.395 Chirality : 0.045 0.345 2038 Planarity : 0.004 0.042 2270 Dihedral : 5.628 65.228 1779 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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 (0.21), residues: 1616 helix: 0.62 (0.23), residues: 513 sheet: -1.00 (0.27), residues: 360 loop : -0.21 (0.24), residues: 743 =============================================================================== Job complete usr+sys time: 2982.64 seconds wall clock time: 55 minutes 10.63 seconds (3310.63 seconds total)