Starting phenix.real_space_refine on Wed Sep 25 18:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/09_2024/8f2b_28812.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/09_2024/8f2b_28812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/09_2024/8f2b_28812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/09_2024/8f2b_28812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/09_2024/8f2b_28812.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/09_2024/8f2b_28812.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 6643 2.51 5 N 1740 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10360 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 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: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 817 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "P" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 277 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3025 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Unusual residues: {'NAG': 3, 'P42': 1, 'PLM': 8, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 6.94, per 1000 atoms: 0.67 Number of scatterers: 10360 At special positions: 0 Unit cell: (111.15, 99.45, 149.5, 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 74 16.00 P 1 15.00 O 1902 8.00 N 1740 7.00 C 6643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 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 E 28 " - pdb=" SG CYS E 82 " distance=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 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 - 3.00 Amino acid : True - 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=2, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 125 " " NAG R 503 " - " ASN R 130 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 45.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.618A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.547A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.802A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.615A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.608A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.585A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.895A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Proline residue: E 38 - end of helix removed outlier: 3.549A pdb=" N MET E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 51 " --> pdb=" O MET E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 62 through 80 removed outlier: 3.668A pdb=" N MET E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.788A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 141 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.551A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.533A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.613A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.614A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 282 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.404A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.416A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.631A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.772A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.350A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.836A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AB5, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.580A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1446 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: 2.88 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1642 1.31 - 1.44: 2930 1.44 - 1.56: 5884 1.56 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 10562 Sorted by residual: bond pdb=" C02 D6M P 101 " pdb=" N03 D6M P 101 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C LYS P 21 " pdb=" O LYS P 21 " ideal model delta sigma weight residual 1.234 1.187 0.046 1.44e-02 4.82e+03 1.04e+01 bond pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.98e+00 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" N VAL E 80 " pdb=" CA VAL E 80 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 ... (remaining 10557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13865 1.41 - 2.82: 340 2.82 - 4.23: 61 4.23 - 5.65: 18 5.65 - 7.06: 2 Bond angle restraints: 14286 Sorted by residual: angle pdb=" N GLU E 76 " pdb=" CA GLU E 76 " pdb=" C GLU E 76 " ideal model delta sigma weight residual 111.07 106.17 4.90 1.07e+00 8.73e-01 2.10e+01 angle pdb=" CA TRP E 84 " pdb=" C TRP E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 118.23 121.65 -3.42 9.20e-01 1.18e+00 1.38e+01 angle pdb=" N GLU R 255 " pdb=" CA GLU R 255 " pdb=" C GLU R 255 " ideal model delta sigma weight residual 113.97 109.43 4.54 1.28e+00 6.10e-01 1.26e+01 angle pdb=" N VAL E 80 " pdb=" CA VAL E 80 " pdb=" C VAL E 80 " ideal model delta sigma weight residual 113.07 108.79 4.28 1.36e+00 5.41e-01 9.88e+00 angle pdb=" C ASN E 29 " pdb=" CA ASN E 29 " pdb=" CB ASN E 29 " ideal model delta sigma weight residual 110.19 105.06 5.13 1.64e+00 3.72e-01 9.78e+00 ... (remaining 14281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 6094 24.30 - 48.60: 286 48.60 - 72.90: 57 72.90 - 97.20: 7 97.20 - 121.50: 4 Dihedral angle restraints: 6448 sinusoidal: 2739 harmonic: 3709 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 93.00 141.79 -48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 131.10 -38.10 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CAI P42 R 512 " pdb=" CAJ P42 R 512 " pdb=" CAK P42 R 512 " pdb=" CAL P42 R 512 " ideal model delta sinusoidal sigma weight residual 179.92 58.42 121.50 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 6445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1270 0.050 - 0.100: 251 0.100 - 0.150: 47 0.150 - 0.200: 6 0.200 - 0.250: 3 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA TYR E 83 " pdb=" N TYR E 83 " pdb=" C TYR E 83 " pdb=" CB TYR E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL E 79 " pdb=" CA VAL E 79 " pdb=" CG1 VAL E 79 " pdb=" CG2 VAL E 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASN E 29 " pdb=" N ASN E 29 " pdb=" C ASN E 29 " pdb=" CB ASN E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1574 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO B 236 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 37 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO E 38 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO G 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.019 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2808 2.80 - 3.33: 9321 3.33 - 3.85: 17500 3.85 - 4.38: 21502 4.38 - 4.90: 35815 Nonbonded interactions: 86946 Sorted by model distance: nonbonded pdb=" O SER A 352 " pdb=" OG SER A 352 " model vdw 2.278 3.040 nonbonded pdb=" O SER P 20 " pdb=" OG SER P 20 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLN R 227 " pdb=" O HOH R 601 " model vdw 2.303 3.040 nonbonded pdb=" OD2 ASP R 373 " pdb=" O HOH R 602 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLU R 240 " pdb=" O HOH R 603 " model vdw 2.312 3.040 ... (remaining 86941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 2.560 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: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.112 10562 Z= 0.262 Angle : 0.554 7.057 14286 Z= 0.324 Chirality : 0.043 0.250 1577 Planarity : 0.003 0.039 1793 Dihedral : 14.226 121.499 4022 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.32 % Allowed : 12.56 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.02 (0.20), residues: 1255 helix: -1.84 (0.17), residues: 504 sheet: -0.17 (0.31), residues: 234 loop : -1.17 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS A 387 PHE 0.010 0.001 PHE B 151 TYR 0.015 0.001 TYR E 83 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4201 (mmp) cc_final: 0.3710 (mpp) REVERT: R 261 TRP cc_start: 0.5889 (m100) cc_final: 0.5634 (m100) REVERT: R 327 MET cc_start: 0.7279 (mtm) cc_final: 0.6728 (mmm) REVERT: R 374 TYR cc_start: 0.6131 (m-80) cc_final: 0.5923 (m-80) outliers start: 14 outliers final: 1 residues processed: 215 average time/residue: 1.6608 time to fit residues: 380.4414 Evaluate side-chains 156 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 59 GLN A 294 GLN B 13 GLN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN N 82 GLN N 84 ASN P 14 ASN R 93 GLN R 179 GLN R 186 ASN R 223 HIS R 257 GLN R 318 ASN R 408 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10562 Z= 0.310 Angle : 0.701 7.789 14286 Z= 0.375 Chirality : 0.047 0.158 1577 Planarity : 0.006 0.040 1793 Dihedral : 11.108 175.149 1774 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.12 % Allowed : 13.31 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.25 (0.23), residues: 1255 helix: 0.82 (0.22), residues: 503 sheet: 0.10 (0.32), residues: 253 loop : -0.33 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 211 HIS 0.008 0.002 HIS B 266 PHE 0.016 0.003 PHE A 222 TYR 0.014 0.002 TYR R 146 ARG 0.008 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.247 Fit side-chains REVERT: A 60 MET cc_start: 0.4237 (mmp) cc_final: 0.3945 (mpp) REVERT: B 59 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: B 96 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7274 (mtm-85) REVERT: N 3 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: N 34 MET cc_start: 0.8804 (mmm) cc_final: 0.8275 (mmm) REVERT: R 141 LYS cc_start: 0.5065 (mmtt) cc_final: 0.4823 (tttt) REVERT: R 261 TRP cc_start: 0.6075 (m100) cc_final: 0.5750 (m100) REVERT: R 361 TRP cc_start: 0.6809 (t-100) cc_final: 0.6301 (t-100) REVERT: R 374 TYR cc_start: 0.6023 (m-80) cc_final: 0.5767 (m-80) outliers start: 33 outliers final: 10 residues processed: 179 average time/residue: 1.6327 time to fit residues: 309.3071 Evaluate side-chains 147 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 268 ASN N 5 GLN N 13 GLN R 179 GLN R 223 HIS R 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10562 Z= 0.192 Angle : 0.567 7.906 14286 Z= 0.303 Chirality : 0.042 0.142 1577 Planarity : 0.004 0.042 1793 Dihedral : 9.963 141.287 1772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.64 % Allowed : 15.20 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.82 (0.24), residues: 1255 helix: 1.52 (0.22), residues: 513 sheet: 0.15 (0.32), residues: 252 loop : -0.18 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.012 0.002 PHE B 151 TYR 0.010 0.001 TYR R 191 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6984 (mmt90) REVERT: A 60 MET cc_start: 0.4348 (mmp) cc_final: 0.3942 (mpp) REVERT: N 3 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: N 105 ARG cc_start: 0.6430 (mtm-85) cc_final: 0.5946 (ttm110) REVERT: R 141 LYS cc_start: 0.5120 (mmtt) cc_final: 0.4916 (tttt) REVERT: R 198 ILE cc_start: 0.6137 (mt) cc_final: 0.5908 (mm) REVERT: R 261 TRP cc_start: 0.6118 (m100) cc_final: 0.5792 (m100) REVERT: R 361 TRP cc_start: 0.6755 (t-100) cc_final: 0.6327 (t-100) REVERT: R 374 TYR cc_start: 0.5991 (m-80) cc_final: 0.5737 (m-80) outliers start: 28 outliers final: 12 residues processed: 156 average time/residue: 1.6319 time to fit residues: 269.9843 Evaluate side-chains 151 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 268 ASN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10562 Z= 0.196 Angle : 0.569 6.784 14286 Z= 0.303 Chirality : 0.042 0.143 1577 Planarity : 0.004 0.043 1793 Dihedral : 10.048 136.599 1772 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.21 % Allowed : 14.45 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.00 (0.24), residues: 1255 helix: 1.69 (0.22), residues: 523 sheet: 0.17 (0.32), residues: 249 loop : -0.10 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.012 0.002 PHE B 151 TYR 0.010 0.002 TYR R 92 ARG 0.005 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4307 (mmp) cc_final: 0.3907 (mpp) REVERT: A 352 SER cc_start: 0.6559 (OUTLIER) cc_final: 0.6295 (p) REVERT: N 3 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: R 198 ILE cc_start: 0.6149 (mt) cc_final: 0.5931 (mm) REVERT: R 361 TRP cc_start: 0.6743 (t-100) cc_final: 0.6326 (t-100) outliers start: 34 outliers final: 17 residues processed: 151 average time/residue: 1.5234 time to fit residues: 244.3320 Evaluate side-chains 153 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10562 Z= 0.199 Angle : 0.571 6.340 14286 Z= 0.304 Chirality : 0.042 0.142 1577 Planarity : 0.004 0.043 1793 Dihedral : 10.227 134.702 1772 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.93 % Allowed : 15.11 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1255 helix: 1.74 (0.22), residues: 526 sheet: 0.10 (0.32), residues: 246 loop : -0.07 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 PHE 0.013 0.002 PHE B 151 TYR 0.019 0.002 TYR R 338 ARG 0.006 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4321 (mmp) cc_final: 0.3919 (mpp) REVERT: B 96 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7120 (mtm-85) REVERT: N 3 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: R 196 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5115 (mmm) REVERT: R 198 ILE cc_start: 0.6156 (mt) cc_final: 0.5920 (mm) REVERT: R 361 TRP cc_start: 0.6716 (t-100) cc_final: 0.6313 (t-100) outliers start: 31 outliers final: 16 residues processed: 149 average time/residue: 1.3910 time to fit residues: 220.5023 Evaluate side-chains 151 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.0270 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.0030 chunk 113 optimal weight: 1.9990 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 88 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN R 179 GLN R 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10562 Z= 0.126 Angle : 0.476 6.071 14286 Z= 0.254 Chirality : 0.040 0.139 1577 Planarity : 0.004 0.045 1793 Dihedral : 9.284 123.596 1772 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.70 % Allowed : 16.24 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.39 (0.24), residues: 1255 helix: 2.19 (0.23), residues: 524 sheet: 0.25 (0.33), residues: 234 loop : -0.04 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.010 0.001 PHE A 212 TYR 0.019 0.001 TYR R 338 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4141 (mmp) cc_final: 0.3796 (mpp) REVERT: N 3 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: N 105 ARG cc_start: 0.6384 (mpp80) cc_final: 0.5878 (ttm110) REVERT: R 198 ILE cc_start: 0.6184 (mt) cc_final: 0.5960 (mm) REVERT: R 229 MET cc_start: 0.6904 (tpp) cc_final: 0.6667 (tpp) REVERT: R 361 TRP cc_start: 0.6652 (t-100) cc_final: 0.6262 (t-100) REVERT: R 374 TYR cc_start: 0.5885 (m-80) cc_final: 0.5627 (m-80) outliers start: 18 outliers final: 7 residues processed: 140 average time/residue: 1.5723 time to fit residues: 233.1855 Evaluate side-chains 139 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.0050 chunk 67 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 54 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10562 Z= 0.118 Angle : 0.463 9.761 14286 Z= 0.244 Chirality : 0.039 0.136 1577 Planarity : 0.004 0.046 1793 Dihedral : 8.757 113.164 1772 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.42 % Allowed : 16.62 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.54 (0.24), residues: 1255 helix: 2.33 (0.23), residues: 531 sheet: 0.42 (0.33), residues: 231 loop : -0.07 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS R 302 PHE 0.009 0.001 PHE A 212 TYR 0.019 0.001 TYR R 338 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7353 (tp40) cc_final: 0.6931 (tp40) REVERT: A 60 MET cc_start: 0.4021 (mmp) cc_final: 0.3735 (mpp) REVERT: N 105 ARG cc_start: 0.6338 (mpp80) cc_final: 0.5845 (ttm110) REVERT: R 198 ILE cc_start: 0.6165 (mt) cc_final: 0.5949 (mm) REVERT: R 229 MET cc_start: 0.6879 (tpp) cc_final: 0.6671 (tpp) REVERT: R 293 VAL cc_start: 0.6715 (m) cc_final: 0.6373 (p) REVERT: R 361 TRP cc_start: 0.6578 (t-100) cc_final: 0.6239 (t-100) REVERT: R 374 TYR cc_start: 0.5860 (m-80) cc_final: 0.5582 (m-80) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 1.4788 time to fit residues: 226.5326 Evaluate side-chains 138 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 268 ASN N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10562 Z= 0.143 Angle : 0.504 9.123 14286 Z= 0.265 Chirality : 0.040 0.150 1577 Planarity : 0.004 0.046 1793 Dihedral : 8.914 118.247 1772 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.61 % Allowed : 16.05 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.59 (0.24), residues: 1255 helix: 2.39 (0.23), residues: 524 sheet: 0.29 (0.33), residues: 235 loop : 0.06 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 336 PHE 0.010 0.001 PHE A 212 TYR 0.019 0.001 TYR R 338 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4075 (mmp) cc_final: 0.3751 (mpp) REVERT: N 105 ARG cc_start: 0.6370 (mpp80) cc_final: 0.5847 (ttm110) REVERT: R 198 ILE cc_start: 0.6159 (mt) cc_final: 0.5908 (mm) REVERT: R 361 TRP cc_start: 0.6567 (t-100) cc_final: 0.6198 (t-100) REVERT: R 374 TYR cc_start: 0.5883 (m-80) cc_final: 0.5607 (m-80) outliers start: 17 outliers final: 8 residues processed: 136 average time/residue: 1.4338 time to fit residues: 207.9036 Evaluate side-chains 132 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 0.0170 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 86 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 390 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10562 Z= 0.206 Angle : 0.585 10.043 14286 Z= 0.306 Chirality : 0.043 0.153 1577 Planarity : 0.004 0.050 1793 Dihedral : 9.690 130.370 1772 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.61 % Allowed : 16.05 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.31 (0.24), residues: 1255 helix: 2.07 (0.22), residues: 527 sheet: 0.21 (0.33), residues: 237 loop : -0.03 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.003 0.001 HIS R 377 PHE 0.011 0.002 PHE B 151 TYR 0.019 0.002 TYR R 338 ARG 0.005 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4187 (mmp) cc_final: 0.3905 (mpp) REVERT: N 105 ARG cc_start: 0.6459 (mpp80) cc_final: 0.5894 (ttm110) REVERT: R 198 ILE cc_start: 0.6109 (mt) cc_final: 0.5884 (mm) REVERT: R 361 TRP cc_start: 0.6583 (t-100) cc_final: 0.6222 (t-100) REVERT: R 399 GLN cc_start: 0.6216 (OUTLIER) cc_final: 0.5841 (mt0) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 1.5436 time to fit residues: 229.9053 Evaluate side-chains 139 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 399 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 0.0040 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 16 ASN B 268 ASN N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10562 Z= 0.128 Angle : 0.494 10.387 14286 Z= 0.257 Chirality : 0.040 0.146 1577 Planarity : 0.004 0.049 1793 Dihedral : 8.786 115.725 1772 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.13 % Allowed : 16.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.57 (0.24), residues: 1255 helix: 2.31 (0.22), residues: 529 sheet: 0.32 (0.33), residues: 235 loop : 0.07 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.010 0.001 PHE A 212 TYR 0.020 0.001 TYR R 338 ARG 0.007 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4020 (mmp) cc_final: 0.3765 (mpp) REVERT: N 105 ARG cc_start: 0.6358 (mpp80) cc_final: 0.5816 (ttm110) REVERT: R 198 ILE cc_start: 0.6156 (mt) cc_final: 0.5925 (mm) REVERT: R 293 VAL cc_start: 0.6733 (m) cc_final: 0.6404 (p) REVERT: R 361 TRP cc_start: 0.6516 (t-100) cc_final: 0.6154 (t-100) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 1.5266 time to fit residues: 220.6392 Evaluate side-chains 138 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 16 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.220832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.190527 restraints weight = 8081.251| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 0.72 r_work: 0.3941 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10562 Z= 0.166 Angle : 0.537 8.754 14286 Z= 0.282 Chirality : 0.041 0.150 1577 Planarity : 0.004 0.050 1793 Dihedral : 9.240 124.256 1772 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.42 % Allowed : 16.24 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1255 helix: 2.25 (0.22), residues: 528 sheet: 0.28 (0.32), residues: 235 loop : 0.03 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.011 0.001 PHE A 212 TYR 0.022 0.001 TYR R 338 ARG 0.007 0.000 ARG P 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.84 seconds wall clock time: 86 minutes 26.97 seconds (5186.97 seconds total)