Starting phenix.real_space_refine on Sun Nov 17 19:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/11_2024/8g4d_29717.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/11_2024/8g4d_29717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/11_2024/8g4d_29717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/11_2024/8g4d_29717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/11_2024/8g4d_29717.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/11_2024/8g4d_29717.cif" } resolution = 3.6 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= 0.001 sd= 0.014 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 6 5.49 5 S 64 5.16 5 C 9315 2.51 5 N 2390 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14402 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1932 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "C" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1932 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.61, per 1000 atoms: 0.60 Number of scatterers: 14402 At special positions: 0 Unit cell: (102.896, 124.696, 178.76, 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 64 16.00 P 6 15.00 O 2627 8.00 N 2390 7.00 C 9315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.9 seconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 13 sheets defined 62.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 40 Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 54 through 82 removed outlier: 4.225A pdb=" N LYS A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 96 through 127 removed outlier: 3.733A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.673A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 225 removed outlier: 4.291A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.554A pdb=" N PHE A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 290 through 316 removed outlier: 3.534A pdb=" N THR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.598A pdb=" N THR A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 513 through 556 removed outlier: 4.544A pdb=" N ALA A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 571 through 602 Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 613 through 644 removed outlier: 4.539A pdb=" N ILE A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 4.091A pdb=" N LYS B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 112 removed outlier: 4.063A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.656A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 4.550A pdb=" N HIS B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.891A pdb=" N LEU B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.713A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 4.682A pdb=" N ASP C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 Processing helix chain 'C' and resid 175 through 193 removed outlier: 4.050A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.986A pdb=" N LEU C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 30 Processing helix chain 'D' and resid 35 through 72 removed outlier: 4.047A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 3.870A pdb=" N ALA D 78 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 79 " --> pdb=" O VAL D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 79' Processing helix chain 'D' and resid 84 through 138 Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 143 through 169 Processing helix chain 'D' and resid 170 through 175 removed outlier: 5.034A pdb=" N GLU D 173 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 236 Processing helix chain 'D' and resid 264 through 273 removed outlier: 3.522A pdb=" N VAL D 268 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 4.167A pdb=" N PHE D 272 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.808A pdb=" N TYR D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 327 through 334 removed outlier: 3.766A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.569A pdb=" N ILE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 Processing helix chain 'E' and resid 38 through 61 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 79 removed outlier: 4.308A pdb=" N ILE E 79 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 138 removed outlier: 4.093A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 170 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.526A pdb=" N ASP E 175 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 218 through 236 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.520A pdb=" N ASP E 284 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 300 removed outlier: 4.059A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.630A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 485 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 356 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 484 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.638A pdb=" N LEU A 359 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 458 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 26 removed outlier: 6.385A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 24 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 9 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 7 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 4 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 26 removed outlier: 6.385A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 24 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 9 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 7 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA B 6 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS B 65 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS B 8 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR B 63 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.419A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP B 168 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 201 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE B 216 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET B 39 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 213 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B 224 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 215 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 26 removed outlier: 6.815A pdb=" N LYS C 11 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS C 24 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE C 9 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 26 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA C 6 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS C 65 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS C 8 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR C 63 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AA8, first strand: chain 'C' and resid 164 through 166 removed outlier: 7.366A pdb=" N ILE C 165 " --> pdb=" O ILE C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.560A pdb=" N GLU D 179 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 216 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 181 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 214 " --> pdb=" O ILE D 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 208 removed outlier: 6.650A pdb=" N ASP D 206 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 256 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 311 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 317 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 180 through 182 Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.663A pdb=" N SER E 245 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 305 through 311 removed outlier: 3.802A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2349 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: 4.27 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4573 1.35 - 1.50: 3825 1.50 - 1.65: 6165 1.65 - 1.80: 62 1.80 - 1.95: 54 Bond restraints: 14679 Sorted by residual: bond pdb=" N VAL C 2 " pdb=" CA VAL C 2 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C LYS A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 bond pdb=" N ILE C 3 " pdb=" CA ILE C 3 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.51e+00 bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.22e-02 6.72e+03 7.11e+00 ... (remaining 14674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19464 2.27 - 4.54: 275 4.54 - 6.81: 38 6.81 - 9.08: 12 9.08 - 11.35: 1 Bond angle restraints: 19790 Sorted by residual: angle pdb=" N TYR A 561 " pdb=" CA TYR A 561 " pdb=" C TYR A 561 " ideal model delta sigma weight residual 113.88 106.09 7.79 1.23e+00 6.61e-01 4.01e+01 angle pdb=" N GLU E 83 " pdb=" CA GLU E 83 " pdb=" C GLU E 83 " ideal model delta sigma weight residual 114.56 108.76 5.80 1.27e+00 6.20e-01 2.08e+01 angle pdb=" C GLN D 162 " pdb=" N GLN D 163 " pdb=" CA GLN D 163 " ideal model delta sigma weight residual 122.06 114.59 7.47 1.86e+00 2.89e-01 1.61e+01 angle pdb=" C ILE D 225 " pdb=" N ARG D 226 " pdb=" CA ARG D 226 " ideal model delta sigma weight residual 121.58 114.03 7.55 1.95e+00 2.63e-01 1.50e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 111.36 107.31 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 19785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8510 30.70 - 61.40: 300 61.40 - 92.09: 29 92.09 - 122.79: 0 122.79 - 153.49: 1 Dihedral angle restraints: 8840 sinusoidal: 3616 harmonic: 5224 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual 292.27 138.78 153.49 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA GLY A 604 " pdb=" C GLY A 604 " pdb=" N TRP A 605 " pdb=" CA TRP A 605 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET E 140 " pdb=" C MET E 140 " pdb=" N GLU E 141 " pdb=" CA GLU E 141 " ideal model delta harmonic sigma weight residual -180.00 -160.63 -19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1661 0.042 - 0.085: 443 0.085 - 0.127: 143 0.127 - 0.169: 12 0.169 - 0.212: 3 Chirality restraints: 2262 Sorted by residual: chirality pdb=" CB ILE E 243 " pdb=" CA ILE E 243 " pdb=" CG1 ILE E 243 " pdb=" CG2 ILE E 243 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLN D 163 " pdb=" N GLN D 163 " pdb=" C GLN D 163 " pdb=" CB GLN D 163 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CB ILE C 3 " pdb=" CA ILE C 3 " pdb=" CG1 ILE C 3 " pdb=" CG2 ILE C 3 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 2259 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 122 " -0.011 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E 122 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 122 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP E 122 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP E 122 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 122 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 122 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 122 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 122 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 122 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 605 " 0.021 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 605 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 605 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 605 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 605 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 605 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " -0.022 2.00e-02 2.50e+03 1.43e-02 5.14e+00 pdb=" CG TRP E 153 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " -0.003 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2290 2.76 - 3.30: 14519 3.30 - 3.83: 23360 3.83 - 4.37: 25816 4.37 - 4.90: 44532 Nonbonded interactions: 110517 Sorted by model distance: nonbonded pdb=" OE1 GLN E 247 " pdb=" OG1 THR E 252 " model vdw 2.228 3.040 nonbonded pdb=" O THR D 128 " pdb=" OG1 THR D 131 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN C 95 " pdb=" NH2 ARG C 156 " model vdw 2.248 3.120 nonbonded pdb=" NH2 ARG A 9 " pdb=" O THR C 99 " model vdw 2.249 3.120 nonbonded pdb=" O ARG E 226 " pdb=" OG1 THR E 230 " model vdw 2.251 3.040 ... (remaining 110512 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 32.790 Find NCS groups from input model: 0.310 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.003 0.061 14679 Z= 0.207 Angle : 0.679 11.346 19790 Z= 0.383 Chirality : 0.043 0.212 2262 Planarity : 0.004 0.067 2467 Dihedral : 15.325 153.488 5458 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.64 % Allowed : 0.45 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1783 helix: 1.43 (0.17), residues: 1017 sheet: -2.67 (0.45), residues: 116 loop : -1.72 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP E 122 HIS 0.013 0.001 HIS E 157 PHE 0.021 0.001 PHE A 501 TYR 0.021 0.001 TYR A 638 ARG 0.016 0.001 ARG E 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8205 (t0) cc_final: 0.7860 (t0) REVERT: C 95 ASN cc_start: 0.7965 (p0) cc_final: 0.7749 (p0) REVERT: C 117 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6569 (tppt) REVERT: D 23 MET cc_start: 0.7397 (ptm) cc_final: 0.6957 (ptt) REVERT: D 169 ILE cc_start: 0.7642 (pt) cc_final: 0.7326 (tp) REVERT: E 112 LEU cc_start: 0.7911 (tp) cc_final: 0.7695 (tt) REVERT: E 120 MET cc_start: 0.8340 (tpt) cc_final: 0.7997 (tpp) REVERT: E 157 HIS cc_start: 0.8354 (p90) cc_final: 0.8079 (p90) outliers start: 10 outliers final: 0 residues processed: 223 average time/residue: 0.2413 time to fit residues: 81.9764 Evaluate side-chains 159 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 160 HIS ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14679 Z= 0.211 Angle : 0.632 9.025 19790 Z= 0.332 Chirality : 0.043 0.179 2262 Planarity : 0.004 0.064 2467 Dihedral : 7.821 153.041 1943 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.02 % Allowed : 7.98 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1783 helix: 1.54 (0.17), residues: 1015 sheet: -2.67 (0.40), residues: 148 loop : -1.50 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 153 HIS 0.010 0.001 HIS E 134 PHE 0.025 0.001 PHE A 223 TYR 0.019 0.001 TYR A 623 ARG 0.008 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7428 (ttt) REVERT: E 157 HIS cc_start: 0.8326 (p90) cc_final: 0.7907 (p-80) outliers start: 16 outliers final: 11 residues processed: 179 average time/residue: 0.2560 time to fit residues: 68.8602 Evaluate side-chains 166 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 109 optimal weight: 0.1980 chunk 44 optimal weight: 30.0000 chunk 161 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 602 GLN B 29 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 105 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 14679 Z= 0.594 Angle : 0.876 10.756 19790 Z= 0.458 Chirality : 0.050 0.206 2262 Planarity : 0.005 0.074 2467 Dihedral : 8.043 142.873 1943 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.02 % Favored : 91.87 % Rotamer: Outliers : 2.43 % Allowed : 13.91 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1783 helix: 0.64 (0.16), residues: 1024 sheet: -3.15 (0.38), residues: 148 loop : -1.61 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 605 HIS 0.009 0.002 HIS B 202 PHE 0.035 0.003 PHE C 166 TYR 0.047 0.003 TYR A 314 ARG 0.009 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.8055 (ptt) cc_final: 0.7818 (ptt) REVERT: B 221 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6665 (mtt) REVERT: C 39 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7867 (ttt) REVERT: D 67 LEU cc_start: 0.5062 (tp) cc_final: 0.4450 (tt) REVERT: D 163 GLN cc_start: 0.6376 (tt0) cc_final: 0.5917 (mp10) REVERT: E 157 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8053 (p-80) outliers start: 38 outliers final: 27 residues processed: 169 average time/residue: 0.2443 time to fit residues: 62.6440 Evaluate side-chains 166 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 157 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 384 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 165 HIS E 19 GLN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14679 Z= 0.229 Angle : 0.638 10.474 19790 Z= 0.333 Chirality : 0.042 0.202 2262 Planarity : 0.004 0.054 2467 Dihedral : 7.794 148.814 1943 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.83 % Rotamer: Outliers : 2.55 % Allowed : 16.02 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1783 helix: 1.26 (0.16), residues: 1025 sheet: -2.97 (0.39), residues: 148 loop : -1.49 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 605 HIS 0.005 0.001 HIS E 134 PHE 0.030 0.002 PHE A 501 TYR 0.018 0.001 TYR A 623 ARG 0.005 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: C 39 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7528 (ttt) REVERT: D 67 LEU cc_start: 0.4306 (tp) cc_final: 0.3224 (tt) REVERT: E 19 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.4796 (mt0) REVERT: E 46 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.6099 (tt) REVERT: E 157 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8222 (p90) outliers start: 40 outliers final: 24 residues processed: 182 average time/residue: 0.2386 time to fit residues: 66.3841 Evaluate side-chains 174 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 157 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 43 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 157 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14679 Z= 0.175 Angle : 0.620 11.614 19790 Z= 0.319 Chirality : 0.042 0.309 2262 Planarity : 0.004 0.072 2467 Dihedral : 7.657 150.969 1943 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.89 % Rotamer: Outliers : 2.62 % Allowed : 16.85 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1783 helix: 1.54 (0.17), residues: 1014 sheet: -2.74 (0.41), residues: 136 loop : -1.49 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 605 HIS 0.006 0.001 HIS D 165 PHE 0.033 0.001 PHE A 501 TYR 0.015 0.001 TYR A 623 ARG 0.012 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: B 9 ILE cc_start: 0.8253 (mm) cc_final: 0.7820 (mm) REVERT: B 105 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.8016 (t0) REVERT: C 39 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7444 (ttt) REVERT: C 71 MET cc_start: 0.7421 (mmp) cc_final: 0.6082 (tmm) REVERT: E 46 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5994 (tt) outliers start: 41 outliers final: 26 residues processed: 187 average time/residue: 0.2450 time to fit residues: 70.4668 Evaluate side-chains 181 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 151 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14679 Z= 0.203 Angle : 0.620 11.391 19790 Z= 0.319 Chirality : 0.042 0.241 2262 Planarity : 0.004 0.091 2467 Dihedral : 7.606 151.124 1943 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 2.68 % Allowed : 17.61 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1783 helix: 1.57 (0.17), residues: 1017 sheet: -2.68 (0.42), residues: 136 loop : -1.47 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 122 HIS 0.016 0.001 HIS E 157 PHE 0.031 0.001 PHE A 223 TYR 0.017 0.001 TYR A 623 ARG 0.020 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: A 369 MET cc_start: 0.4017 (mmp) cc_final: 0.3446 (mmm) REVERT: B 9 ILE cc_start: 0.8263 (mm) cc_final: 0.7831 (mm) REVERT: B 105 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (t0) REVERT: C 39 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7533 (ttt) REVERT: C 71 MET cc_start: 0.7543 (mmp) cc_final: 0.6028 (tmm) outliers start: 42 outliers final: 31 residues processed: 185 average time/residue: 0.2445 time to fit residues: 69.1787 Evaluate side-chains 189 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 151 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14679 Z= 0.179 Angle : 0.618 15.290 19790 Z= 0.315 Chirality : 0.041 0.219 2262 Planarity : 0.004 0.092 2467 Dihedral : 7.532 152.257 1943 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 2.23 % Allowed : 18.63 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1783 helix: 1.64 (0.17), residues: 1018 sheet: -2.58 (0.42), residues: 136 loop : -1.42 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 122 HIS 0.011 0.001 HIS E 157 PHE 0.038 0.001 PHE A 501 TYR 0.017 0.001 TYR E 293 ARG 0.017 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 338 LYS cc_start: 0.9095 (tptt) cc_final: 0.8853 (tptp) REVERT: A 369 MET cc_start: 0.3887 (mmp) cc_final: 0.3394 (mmm) REVERT: B 9 ILE cc_start: 0.8209 (mm) cc_final: 0.7785 (mm) REVERT: B 105 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7912 (t0) REVERT: C 39 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7461 (ttt) outliers start: 35 outliers final: 26 residues processed: 182 average time/residue: 0.2525 time to fit residues: 69.5970 Evaluate side-chains 184 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 134 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14679 Z= 0.217 Angle : 0.640 14.599 19790 Z= 0.327 Chirality : 0.042 0.218 2262 Planarity : 0.004 0.064 2467 Dihedral : 7.513 151.989 1943 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.17 % Rotamer: Outliers : 1.98 % Allowed : 19.08 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1783 helix: 1.61 (0.17), residues: 1018 sheet: -2.65 (0.39), residues: 159 loop : -1.34 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 122 HIS 0.011 0.001 HIS E 157 PHE 0.036 0.001 PHE A 501 TYR 0.017 0.001 TYR A 623 ARG 0.014 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: A 338 LYS cc_start: 0.9111 (tptt) cc_final: 0.8873 (tptp) REVERT: A 369 MET cc_start: 0.3905 (mmp) cc_final: 0.3161 (mmm) REVERT: A 383 MET cc_start: 0.1344 (tpt) cc_final: -0.0617 (ptm) REVERT: B 9 ILE cc_start: 0.8265 (mm) cc_final: 0.7836 (mm) REVERT: C 39 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7525 (ttt) outliers start: 31 outliers final: 26 residues processed: 178 average time/residue: 0.2419 time to fit residues: 65.3115 Evaluate side-chains 181 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.0070 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14679 Z= 0.175 Angle : 0.631 13.597 19790 Z= 0.321 Chirality : 0.041 0.227 2262 Planarity : 0.004 0.085 2467 Dihedral : 7.457 153.664 1943 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 1.79 % Allowed : 19.40 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1783 helix: 1.68 (0.17), residues: 1019 sheet: -2.52 (0.40), residues: 159 loop : -1.35 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 122 HIS 0.010 0.001 HIS E 157 PHE 0.035 0.001 PHE A 501 TYR 0.015 0.001 TYR A 623 ARG 0.015 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: A 369 MET cc_start: 0.3905 (mmp) cc_final: 0.3249 (mmm) REVERT: B 9 ILE cc_start: 0.8224 (mm) cc_final: 0.7780 (mm) REVERT: C 39 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7454 (ttt) REVERT: C 71 MET cc_start: 0.7332 (mmp) cc_final: 0.5907 (tmm) outliers start: 28 outliers final: 25 residues processed: 176 average time/residue: 0.2667 time to fit residues: 72.0619 Evaluate side-chains 185 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 0.0050 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14679 Z= 0.173 Angle : 0.637 13.592 19790 Z= 0.322 Chirality : 0.041 0.227 2262 Planarity : 0.003 0.056 2467 Dihedral : 7.384 155.786 1943 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 1.85 % Allowed : 19.40 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1783 helix: 1.75 (0.17), residues: 1019 sheet: -2.45 (0.40), residues: 165 loop : -1.27 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 122 HIS 0.010 0.001 HIS E 157 PHE 0.034 0.001 PHE A 223 TYR 0.016 0.001 TYR E 293 ARG 0.013 0.001 ARG C 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: A 369 MET cc_start: 0.3827 (mmp) cc_final: 0.3224 (mmm) REVERT: A 383 MET cc_start: 0.0608 (tpt) cc_final: -0.0911 (ttt) REVERT: B 9 ILE cc_start: 0.8202 (mm) cc_final: 0.7745 (mm) REVERT: C 39 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7442 (ttt) REVERT: C 71 MET cc_start: 0.7385 (mmp) cc_final: 0.5935 (tmm) REVERT: E 157 HIS cc_start: 0.8385 (p-80) cc_final: 0.8171 (p-80) outliers start: 29 outliers final: 25 residues processed: 186 average time/residue: 0.2693 time to fit residues: 76.4085 Evaluate side-chains 192 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 140 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 8 optimal weight: 0.0980 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147516 restraints weight = 25743.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.148717 restraints weight = 39799.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.148974 restraints weight = 25767.742| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14679 Z= 0.164 Angle : 0.631 13.128 19790 Z= 0.318 Chirality : 0.041 0.218 2262 Planarity : 0.003 0.058 2467 Dihedral : 7.308 158.381 1943 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 1.47 % Allowed : 20.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1783 helix: 1.86 (0.17), residues: 1013 sheet: -2.40 (0.40), residues: 165 loop : -1.26 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 122 HIS 0.010 0.001 HIS E 157 PHE 0.033 0.001 PHE A 223 TYR 0.013 0.001 TYR E 64 ARG 0.013 0.000 ARG D 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.73 seconds wall clock time: 50 minutes 35.28 seconds (3035.28 seconds total)