Starting phenix.real_space_refine on Fri Dec 8 20:14:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tch_25812/12_2023/7tch_25812_updated.pdb" } resolution = 3.7 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= 0.026 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 7 5.49 5 S 39 5.16 5 C 5838 2.51 5 N 1491 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 238": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9043 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5078 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 10, 'TRANS': 634} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1922 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "C" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1922 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'I0O': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.59 Number of scatterers: 9043 At special positions: 0 Unit cell: (77.608, 82.84, 156.96, 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 39 16.00 P 7 15.00 O 1668 8.00 N 1491 7.00 C 5838 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 8 sheets defined 49.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.698A pdb=" N LYS A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 18 No H-bonds generated for 'chain 'A' and resid 15 through 18' Processing helix chain 'A' and resid 22 through 39 removed outlier: 3.932A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 53 through 83 removed outlier: 3.999A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 97 through 137 removed outlier: 3.613A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 176 removed outlier: 3.625A pdb=" N VAL A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 removed outlier: 3.731A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 4.061A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 286 through 323 removed outlier: 4.573A pdb=" N LEU A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.809A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 462 through 471 removed outlier: 4.173A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 525 through 556 removed outlier: 3.953A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 removed outlier: 3.674A pdb=" N ILE A 563 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A 564 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG A 565 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 603 removed outlier: 3.896A pdb=" N ILE A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 4.290A pdb=" N SER A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 644 removed outlier: 3.524A pdb=" N MET A 620 " --> pdb=" O MET A 616 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 148 through 158 removed outlier: 4.043A pdb=" N ALA B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.826A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 102 through 111 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.834A pdb=" N ASN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.181A pdb=" N TYR C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.538A pdb=" N VAL A 363 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 424 through 427 removed outlier: 3.529A pdb=" N GLN A 433 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.542A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.850A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 10 through 14 removed outlier: 3.717A pdb=" N LYS B 11 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 23 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR B 13 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU B 21 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.754A pdb=" N THR C 63 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 221 through 225 removed outlier: 3.767A pdb=" N PHE C 215 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 224 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 213 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 197 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE C 38 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET C 199 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 200 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.671A pdb=" N ILE C 9 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 26 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LYS C 11 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS C 24 " --> pdb=" O LYS C 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 380 hydrogen bonds defined for protein. 1113 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: 2.41 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2836 1.34 - 1.46: 1807 1.46 - 1.58: 4465 1.58 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 9194 Sorted by residual: bond pdb=" C23 I0O A 701 " pdb=" C25 I0O A 701 " ideal model delta sigma weight residual 1.602 1.502 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C18 I0O A 701 " pdb=" C20 I0O A 701 " ideal model delta sigma weight residual 1.576 1.502 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C25 I0O A 701 " pdb=" C26 I0O A 701 " ideal model delta sigma weight residual 1.589 1.515 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C26 I0O A 701 " pdb=" C27 I0O A 701 " ideal model delta sigma weight residual 1.566 1.497 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C21 I0O A 701 " pdb=" C22 I0O A 701 " ideal model delta sigma weight residual 1.564 1.496 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 9189 not shown) Histogram of bond angle deviations from ideal: 99.40 - 107.46: 191 107.46 - 115.52: 5760 115.52 - 123.58: 6269 123.58 - 131.63: 147 131.63 - 139.69: 8 Bond angle restraints: 12375 Sorted by residual: angle pdb=" C19 I0O A 701 " pdb=" C18 I0O A 701 " pdb=" C20 I0O A 701 " ideal model delta sigma weight residual 68.21 115.17 -46.96 3.00e+00 1.11e-01 2.45e+02 angle pdb=" C44 I0O A 701 " pdb=" C43 I0O A 701 " pdb=" C45 I0O A 701 " ideal model delta sigma weight residual 68.19 115.07 -46.88 3.00e+00 1.11e-01 2.44e+02 angle pdb=" C24 I0O A 701 " pdb=" C23 I0O A 701 " pdb=" C25 I0O A 701 " ideal model delta sigma weight residual 74.54 114.99 -40.45 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C17 I0O A 701 " pdb=" C18 I0O A 701 " pdb=" C19 I0O A 701 " ideal model delta sigma weight residual 85.83 123.93 -38.10 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C42 I0O A 701 " pdb=" C43 I0O A 701 " pdb=" C45 I0O A 701 " ideal model delta sigma weight residual 85.85 121.32 -35.47 3.00e+00 1.11e-01 1.40e+02 ... (remaining 12370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 5252 27.86 - 55.72: 292 55.72 - 83.58: 37 83.58 - 111.44: 2 111.44 - 139.30: 3 Dihedral angle restraints: 5586 sinusoidal: 2305 harmonic: 3281 Sorted by residual: dihedral pdb=" CA ILE A 273 " pdb=" C ILE A 273 " pdb=" N SER A 274 " pdb=" CA SER A 274 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" C38 I0O A 701 " pdb=" C40 I0O A 701 " pdb=" C41 I0O A 701 " pdb=" C42 I0O A 701 " ideal model delta sinusoidal sigma weight residual 202.30 63.00 139.30 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C12 I0O A 701 " pdb=" C15 I0O A 701 " pdb=" C16 I0O A 701 " pdb=" C17 I0O A 701 " ideal model delta sinusoidal sigma weight residual 197.35 70.80 126.55 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1111 0.047 - 0.093: 250 0.093 - 0.140: 58 0.140 - 0.186: 4 0.186 - 0.233: 3 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE A 273 " pdb=" CA ILE A 273 " pdb=" CG1 ILE A 273 " pdb=" CG2 ILE A 273 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C9 I0O A 701 " pdb=" C10 I0O A 701 " pdb=" C8 I0O A 701 " pdb=" N16 I0O A 701 " both_signs ideal model delta sigma weight residual False -2.58 -2.38 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1423 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 I0O A 701 " -0.117 2.00e-02 2.50e+03 9.58e-02 1.15e+02 pdb=" C13 I0O A 701 " 0.021 2.00e-02 2.50e+03 pdb=" C2 I0O A 701 " 0.151 2.00e-02 2.50e+03 pdb=" C3 I0O A 701 " 0.034 2.00e-02 2.50e+03 pdb=" C4 I0O A 701 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 I0O A 701 " 0.054 2.00e-02 2.50e+03 4.51e-02 2.54e+01 pdb=" C27 I0O A 701 " -0.068 2.00e-02 2.50e+03 pdb=" C28 I0O A 701 " -0.024 2.00e-02 2.50e+03 pdb=" C29 I0O A 701 " -0.006 2.00e-02 2.50e+03 pdb=" C30 I0O A 701 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 I0O A 701 " 0.038 2.00e-02 2.50e+03 2.48e-02 7.70e+00 pdb=" C12 I0O A 701 " 0.013 2.00e-02 2.50e+03 pdb=" C14 I0O A 701 " 0.003 2.00e-02 2.50e+03 pdb=" C15 I0O A 701 " -0.024 2.00e-02 2.50e+03 pdb=" C5 I0O A 701 " -0.030 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1821 2.78 - 3.31: 8516 3.31 - 3.84: 13735 3.84 - 4.37: 15060 4.37 - 4.90: 26946 Nonbonded interactions: 66078 Sorted by model distance: nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.246 2.440 nonbonded pdb=" OD2 ASP B 70 " pdb=" OG1 THR B 72 " model vdw 2.249 2.440 nonbonded pdb=" O SER A 188 " pdb=" ND2 ASN B 142 " model vdw 2.265 2.520 nonbonded pdb=" O TYR B 222 " pdb=" OG1 THR B 223 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR A 216 " pdb=" ND1 HIS A 596 " model vdw 2.297 2.520 ... (remaining 66073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.020 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.380 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.005 0.100 9194 Z= 0.323 Angle : 1.165 46.957 12375 Z= 0.457 Chirality : 0.043 0.233 1426 Planarity : 0.004 0.096 1534 Dihedral : 16.678 139.295 3476 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1129 helix: 1.83 (0.22), residues: 570 sheet: -0.31 (0.56), residues: 111 loop : -2.35 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 605 HIS 0.002 0.001 HIS C 160 PHE 0.018 0.001 PHE A 27 TYR 0.015 0.001 TYR A 627 ARG 0.009 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.077 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2124 time to fit residues: 46.9921 Evaluate side-chains 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 0.0270 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9194 Z= 0.143 Angle : 0.606 21.774 12375 Z= 0.285 Chirality : 0.040 0.141 1426 Planarity : 0.003 0.045 1534 Dihedral : 11.922 132.837 1301 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.12 % Allowed : 8.65 % Favored : 90.23 % 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: 0.23 (0.27), residues: 1129 helix: 2.02 (0.23), residues: 574 sheet: -0.97 (0.49), residues: 131 loop : -2.22 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.025 0.001 PHE A 27 TYR 0.018 0.001 TYR A 437 ARG 0.004 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.129 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 142 average time/residue: 0.2172 time to fit residues: 42.9038 Evaluate side-chains 139 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0884 time to fit residues: 2.5151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 28 optimal weight: 0.0070 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9194 Z= 0.232 Angle : 0.641 22.684 12375 Z= 0.304 Chirality : 0.041 0.212 1426 Planarity : 0.003 0.042 1534 Dihedral : 10.711 130.914 1301 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.53 % Allowed : 12.51 % Favored : 85.96 % 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: -0.04 (0.26), residues: 1129 helix: 1.81 (0.23), residues: 578 sheet: -1.19 (0.50), residues: 121 loop : -2.36 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 605 HIS 0.002 0.001 HIS B 29 PHE 0.023 0.001 PHE A 27 TYR 0.012 0.001 TYR A 627 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.042 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 146 average time/residue: 0.2213 time to fit residues: 45.1409 Evaluate side-chains 138 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0856 time to fit residues: 3.7146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9194 Z= 0.211 Angle : 0.612 22.482 12375 Z= 0.294 Chirality : 0.040 0.154 1426 Planarity : 0.003 0.041 1534 Dihedral : 10.208 128.117 1301 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.61 % Allowed : 14.45 % Favored : 84.94 % 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: 0.00 (0.26), residues: 1129 helix: 1.82 (0.23), residues: 577 sheet: -0.80 (0.51), residues: 118 loop : -2.40 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 605 HIS 0.002 0.001 HIS C 160 PHE 0.022 0.001 PHE A 27 TYR 0.012 0.001 TYR A 584 ARG 0.005 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.157 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 135 average time/residue: 0.2216 time to fit residues: 42.0707 Evaluate side-chains 129 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0877 time to fit residues: 2.2272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9194 Z= 0.166 Angle : 0.593 22.390 12375 Z= 0.282 Chirality : 0.039 0.136 1426 Planarity : 0.003 0.040 1534 Dihedral : 9.848 125.734 1301 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.51 % Allowed : 15.97 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1129 helix: 1.94 (0.23), residues: 566 sheet: -0.68 (0.52), residues: 118 loop : -2.31 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.023 0.001 PHE A 483 TYR 0.020 0.001 TYR A 547 ARG 0.004 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.125 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 130 average time/residue: 0.2187 time to fit residues: 39.7763 Evaluate side-chains 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0906 time to fit residues: 2.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9194 Z= 0.194 Angle : 0.615 22.204 12375 Z= 0.293 Chirality : 0.040 0.142 1426 Planarity : 0.003 0.038 1534 Dihedral : 9.775 123.821 1301 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.02 % Allowed : 16.07 % Favored : 82.91 % 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: 0.03 (0.26), residues: 1129 helix: 1.89 (0.23), residues: 568 sheet: -0.77 (0.50), residues: 128 loop : -2.42 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.025 0.001 PHE A 483 TYR 0.014 0.001 TYR A 547 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.091 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 137 average time/residue: 0.2133 time to fit residues: 41.2268 Evaluate side-chains 134 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0854 time to fit residues: 2.2622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0270 chunk 61 optimal weight: 0.0050 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 overall best weight: 0.3452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9194 Z= 0.129 Angle : 0.595 21.981 12375 Z= 0.275 Chirality : 0.039 0.127 1426 Planarity : 0.002 0.038 1534 Dihedral : 9.237 120.399 1301 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.20 % Allowed : 18.11 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1129 helix: 2.09 (0.23), residues: 563 sheet: -0.56 (0.52), residues: 118 loop : -2.32 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.018 0.001 PHE A 483 TYR 0.013 0.001 TYR A 584 ARG 0.003 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.903 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.2127 time to fit residues: 42.8259 Evaluate side-chains 126 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 0.0020 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9194 Z= 0.151 Angle : 0.606 21.737 12375 Z= 0.283 Chirality : 0.039 0.142 1426 Planarity : 0.003 0.038 1534 Dihedral : 9.101 118.242 1301 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.81 % Allowed : 19.53 % Favored : 79.65 % 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: 0.29 (0.27), residues: 1129 helix: 2.08 (0.23), residues: 567 sheet: -0.50 (0.52), residues: 118 loop : -2.27 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.017 0.001 PHE A 27 TYR 0.024 0.001 TYR A 437 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.954 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 124 average time/residue: 0.2241 time to fit residues: 38.5098 Evaluate side-chains 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0861 time to fit residues: 2.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9194 Z= 0.205 Angle : 0.640 21.664 12375 Z= 0.299 Chirality : 0.040 0.142 1426 Planarity : 0.003 0.037 1534 Dihedral : 9.268 116.451 1301 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.61 % Allowed : 18.72 % Favored : 80.67 % 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: 0.11 (0.26), residues: 1129 helix: 1.90 (0.23), residues: 570 sheet: -0.49 (0.52), residues: 118 loop : -2.35 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.021 0.001 PHE A 27 TYR 0.011 0.001 TYR A 584 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.059 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 140 average time/residue: 0.2107 time to fit residues: 41.8298 Evaluate side-chains 129 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0923 time to fit residues: 2.0805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9194 Z= 0.138 Angle : 0.623 21.605 12375 Z= 0.289 Chirality : 0.039 0.130 1426 Planarity : 0.003 0.037 1534 Dihedral : 8.896 114.474 1301 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 20.55 % Favored : 79.45 % 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 (0.27), residues: 1129 helix: 2.10 (0.23), residues: 565 sheet: -0.44 (0.53), residues: 118 loop : -2.34 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.001 0.000 HIS C 160 PHE 0.015 0.001 PHE A 27 TYR 0.012 0.001 TYR A 584 ARG 0.002 0.000 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.995 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2200 time to fit residues: 39.6315 Evaluate side-chains 121 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0070 chunk 81 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.0000 chunk 5 optimal weight: 0.3980 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.162018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120040 restraints weight = 10954.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119880 restraints weight = 11925.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121401 restraints weight = 9083.717| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9194 Z= 0.132 Angle : 0.621 21.482 12375 Z= 0.287 Chirality : 0.039 0.145 1426 Planarity : 0.003 0.038 1534 Dihedral : 8.578 112.083 1301 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 20.55 % Favored : 79.45 % 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 (0.27), residues: 1129 helix: 2.18 (0.23), residues: 559 sheet: -0.43 (0.53), residues: 121 loop : -2.20 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 605 HIS 0.001 0.000 HIS C 160 PHE 0.013 0.001 PHE A 329 TYR 0.024 0.001 TYR A 437 ARG 0.002 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.55 seconds wall clock time: 36 minutes 51.32 seconds (2211.32 seconds total)