Starting phenix.real_space_refine on Thu Jul 2 21:48:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.map" model { file = "/net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plw_13504/07_2026/7plw_13504.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1722 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.94, per 1000 atoms: 0.19 Number of scatterers: 10139 At special positions: 0 Unit cell: (107.06, 134.62, 148.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 2 15.00 Mg 1 11.99 O 1889 8.00 N 1722 7.00 C 6462 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 314.2 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 55.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.304A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.555A pdb=" N SER A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.892A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.741A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.983A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.334A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.572A pdb=" N LYS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.667A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.879A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.550A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.764A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.542A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.531A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.829A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.612A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.889A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 removed outlier: 4.068A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.829A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.629A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.073A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 4.457A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 4.067A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.381A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.836A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.728A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.735A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.225A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.502A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.701A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.830A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.995A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 42 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.657A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.448A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.652A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.556A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.417A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 531 hydrogen bonds defined for protein. 1482 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: 1.52 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1694 1.32 - 1.44: 2730 1.44 - 1.56: 5825 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10354 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.198 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.40e-02 5.10e+03 9.55e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.466 0.059 2.10e-02 2.27e+03 7.81e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 10349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 13717 2.45 - 4.90: 233 4.90 - 7.36: 23 7.36 - 9.81: 6 9.81 - 12.26: 3 Bond angle restraints: 13982 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.69 11.01 1.80e+00 3.09e-01 3.74e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 108.88 -5.88 1.10e+00 8.26e-01 2.86e+01 angle pdb=" C TYR A 113 " pdb=" N GLU A 114 " pdb=" CA GLU A 114 " ideal model delta sigma weight residual 121.63 131.46 -9.83 1.92e+00 2.71e-01 2.62e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.20 4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA EEP H 2 " pdb=" CB EEP H 2 " pdb=" CG EEP H 2 " ideal model delta sigma weight residual 115.99 103.73 12.26 3.00e+00 1.11e-01 1.67e+01 ... (remaining 13977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 6079 30.36 - 60.71: 122 60.71 - 91.07: 40 91.07 - 121.43: 0 121.43 - 151.78: 3 Dihedral angle restraints: 6244 sinusoidal: 2554 harmonic: 3690 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.78 -151.78 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 83.00 -143.00 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 175.06 124.95 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 6241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.022: 1526 1.022 - 2.044: 0 2.044 - 3.066: 0 3.066 - 4.089: 0 4.089 - 5.111: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.56 5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.36 4.89 2.00e-01 2.50e+01 5.97e+02 chirality pdb=" CA GLU A 512 " pdb=" N GLU A 512 " pdb=" C GLU A 512 " pdb=" CB GLU A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1525 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 196 " 0.133 9.50e-02 1.11e+02 7.65e-02 3.08e+01 pdb=" NE ARG C 196 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG C 196 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG C 196 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG C 196 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.004 2.00e-02 2.50e+03 3.78e-02 2.86e+01 pdb=" CG TYR C 306 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.113 9.50e-02 1.11e+02 6.59e-02 2.37e+01 pdb=" NE ARG A 677 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.023 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 11 2.37 - 3.00: 5385 3.00 - 3.63: 14911 3.63 - 4.27: 22661 4.27 - 4.90: 37881 Nonbonded interactions: 80849 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OG SER A 78 " pdb=" O ALA A 753 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASP C 11 " pdb=" OG1 THR C 106 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU A 476 " pdb=" NH1 ARG A 701 " model vdw 2.246 3.120 nonbonded pdb=" OD1 ASN C 128 " pdb=" NZ LYS C 359 " model vdw 2.260 3.120 ... (remaining 80844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.000 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.119 10356 Z= 0.235 Angle : 0.845 12.259 13988 Z= 0.500 Chirality : 0.188 5.111 1528 Planarity : 0.008 0.116 1789 Dihedral : 15.080 151.783 3860 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.20), residues: 1236 helix: -1.74 (0.17), residues: 598 sheet: 0.50 (0.39), residues: 144 loop : -0.54 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.011 ARG C 196 TYR 0.075 0.006 TYR A 113 PHE 0.037 0.003 PHE A 564 TRP 0.025 0.003 TRP C 356 HIS 0.011 0.002 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (10354) covalent geometry : angle 0.84104 / 0.50 (13982) hydrogen bonds : bond 0.16410 / 10.75 ( 529) hydrogen bonds : angle 7.21152 / 5.15 ( 1482) link_TRANS : bond 0.00819 / 0.40 ( 2) link_TRANS : angle 3.99825 / 2.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8263 (m-40) cc_final: 0.7988 (m-40) REVERT: B 50 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8839 (pttm) REVERT: B 110 ARG cc_start: 0.9072 (mtt-85) cc_final: 0.8447 (tpp80) REVERT: A 478 MET cc_start: 0.8209 (mmt) cc_final: 0.7822 (mmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1066 time to fit residues: 21.8631 Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 HIS A 149 GLN A 264 GLN A 354 HIS A 463 GLN A 464 GLN A 497 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 775 GLN C 128 ASN C 162 ASN C 280 ASN C 296 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.045761 restraints weight = 43335.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047540 restraints weight = 20486.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048717 restraints weight = 12562.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049501 restraints weight = 8924.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050034 restraints weight = 7040.856| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10356 Z= 0.145 Angle : 0.645 7.340 13988 Z= 0.344 Chirality : 0.043 0.160 1528 Planarity : 0.005 0.058 1789 Dihedral : 8.916 148.996 1386 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.02 % Allowed : 4.34 % Favored : 94.64 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1236 helix: 0.62 (0.20), residues: 614 sheet: 0.82 (0.39), residues: 154 loop : 0.13 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 692 TYR 0.030 0.002 TYR A 113 PHE 0.024 0.002 PHE C 255 TRP 0.022 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10354) covalent geometry : angle 0.64502 / 0.34 (13982) hydrogen bonds : bond 0.04311 / 2.75 ( 529) hydrogen bonds : angle 5.03393 / 3.59 ( 1482) link_TRANS : bond 0.00381 / 0.20 ( 2) link_TRANS : angle 0.99615 / 0.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8396 (m-40) cc_final: 0.8173 (m-40) REVERT: B 110 ARG cc_start: 0.9172 (mtt-85) cc_final: 0.8527 (tpp80) REVERT: A 478 MET cc_start: 0.8787 (mmt) cc_final: 0.7927 (mmt) REVERT: A 490 TYR cc_start: 0.7430 (t80) cc_final: 0.7162 (t80) REVERT: A 511 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8263 (tm-30) outliers start: 11 outliers final: 5 residues processed: 106 average time/residue: 0.0783 time to fit residues: 12.4646 Evaluate side-chains 77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 790 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 GLN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045790 restraints weight = 43216.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047565 restraints weight = 20356.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048745 restraints weight = 12486.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049552 restraints weight = 8889.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050069 restraints weight = 6954.851| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10356 Z= 0.124 Angle : 0.575 8.147 13988 Z= 0.301 Chirality : 0.041 0.177 1528 Planarity : 0.004 0.055 1789 Dihedral : 8.270 145.686 1386 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.92 % Allowed : 5.82 % Favored : 93.25 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1236 helix: 1.21 (0.21), residues: 613 sheet: 0.67 (0.38), residues: 160 loop : 0.26 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 784 TYR 0.019 0.001 TYR A 113 PHE 0.032 0.002 PHE B 12 TRP 0.031 0.002 TRP A 484 HIS 0.010 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10354) covalent geometry : angle 0.57460 / 0.30 (13982) hydrogen bonds : bond 0.03756 / 2.41 ( 529) hydrogen bonds : angle 4.76449 / 3.41 ( 1482) link_TRANS : bond 0.00174 / 0.09 ( 2) link_TRANS : angle 0.44375 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8258 (m-40) cc_final: 0.8017 (m-40) REVERT: B 73 MET cc_start: 0.8014 (tmm) cc_final: 0.7704 (tmm) REVERT: B 110 ARG cc_start: 0.9126 (mtt-85) cc_final: 0.8763 (mtt-85) REVERT: A 478 MET cc_start: 0.8667 (mmt) cc_final: 0.8283 (mmm) REVERT: A 490 TYR cc_start: 0.7601 (t80) cc_final: 0.7343 (t80) REVERT: A 511 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8221 (tm-30) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.0913 time to fit residues: 12.5708 Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 GLN A 657 HIS ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.063426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045599 restraints weight = 43261.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.047365 restraints weight = 20332.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048548 restraints weight = 12447.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049356 restraints weight = 8826.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049872 restraints weight = 6937.648| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10356 Z= 0.123 Angle : 0.565 10.501 13988 Z= 0.291 Chirality : 0.041 0.152 1528 Planarity : 0.004 0.047 1789 Dihedral : 7.891 145.383 1386 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.11 % Allowed : 7.21 % Favored : 91.68 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1236 helix: 1.46 (0.21), residues: 613 sheet: 0.64 (0.38), residues: 160 loop : 0.28 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 784 TYR 0.012 0.001 TYR A 113 PHE 0.019 0.001 PHE C 255 TRP 0.033 0.001 TRP A 484 HIS 0.011 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10354) covalent geometry : angle 0.56454 / 0.29 (13982) hydrogen bonds : bond 0.03521 / 2.28 ( 529) hydrogen bonds : angle 4.61331 / 3.30 ( 1482) link_TRANS : bond 0.00178 / 0.09 ( 2) link_TRANS : angle 0.48274 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8898 (tpp) cc_final: 0.8678 (tpp) REVERT: B 45 ASN cc_start: 0.8232 (m-40) cc_final: 0.7987 (m-40) REVERT: B 73 MET cc_start: 0.7569 (tmm) cc_final: 0.7266 (tmm) REVERT: B 110 ARG cc_start: 0.9138 (mtt-85) cc_final: 0.8608 (tpp80) REVERT: A 364 MET cc_start: 0.9143 (mmt) cc_final: 0.8763 (mmp) REVERT: A 478 MET cc_start: 0.8572 (mmt) cc_final: 0.7659 (mmm) REVERT: A 511 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8272 (tm-30) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.0919 time to fit residues: 11.9163 Evaluate side-chains 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 HIS A 430 HIS A 680 GLN A 730 ASN C 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045121 restraints weight = 43238.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046861 restraints weight = 20379.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048021 restraints weight = 12508.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048809 restraints weight = 8936.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049316 restraints weight = 7042.019| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10356 Z= 0.128 Angle : 0.553 11.466 13988 Z= 0.283 Chirality : 0.041 0.179 1528 Planarity : 0.004 0.050 1789 Dihedral : 7.574 138.448 1386 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.11 % Allowed : 7.76 % Favored : 91.13 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1236 helix: 1.70 (0.22), residues: 608 sheet: 0.55 (0.38), residues: 166 loop : 0.28 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 784 TYR 0.010 0.001 TYR A 113 PHE 0.018 0.001 PHE C 255 TRP 0.045 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10354) covalent geometry : angle 0.55330 / 0.28 (13982) hydrogen bonds : bond 0.03429 / 2.23 ( 529) hydrogen bonds : angle 4.45184 / 3.18 ( 1482) link_TRANS : bond 0.00152 / 0.08 ( 2) link_TRANS : angle 0.44775 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8284 (m-40) cc_final: 0.8054 (m-40) REVERT: B 73 MET cc_start: 0.7458 (tmm) cc_final: 0.7089 (tmm) REVERT: A 310 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8605 (mp-120) REVERT: A 364 MET cc_start: 0.9119 (mmt) cc_final: 0.8840 (mmm) REVERT: A 511 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8305 (tm-30) outliers start: 12 outliers final: 5 residues processed: 78 average time/residue: 0.0959 time to fit residues: 11.0586 Evaluate side-chains 74 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.063608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045666 restraints weight = 43513.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047457 restraints weight = 20422.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048654 restraints weight = 12484.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049423 restraints weight = 8907.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049926 restraints weight = 7046.259| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10356 Z= 0.108 Angle : 0.543 11.214 13988 Z= 0.275 Chirality : 0.040 0.154 1528 Planarity : 0.004 0.052 1789 Dihedral : 7.316 131.470 1386 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 8.60 % Favored : 90.30 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1236 helix: 1.83 (0.22), residues: 607 sheet: 0.62 (0.38), residues: 164 loop : 0.30 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.008 0.001 TYR A 490 PHE 0.017 0.001 PHE C 255 TRP 0.031 0.001 TRP A 484 HIS 0.022 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10354) covalent geometry : angle 0.54290 / 0.28 (13982) hydrogen bonds : bond 0.03312 / 2.16 ( 529) hydrogen bonds : angle 4.36131 / 3.11 ( 1482) link_TRANS : bond 0.00160 / 0.08 ( 2) link_TRANS : angle 0.46348 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8269 (m-40) cc_final: 0.8054 (m-40) REVERT: B 73 MET cc_start: 0.7388 (tmm) cc_final: 0.6966 (tmm) REVERT: B 110 ARG cc_start: 0.9103 (mtt-85) cc_final: 0.8733 (mmt180) REVERT: A 310 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8605 (mp-120) REVERT: A 364 MET cc_start: 0.9111 (mmt) cc_final: 0.8838 (mmm) REVERT: A 478 MET cc_start: 0.8366 (mmm) cc_final: 0.8005 (mmm) REVERT: A 511 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8256 (tm-30) outliers start: 12 outliers final: 3 residues processed: 86 average time/residue: 0.0895 time to fit residues: 11.2503 Evaluate side-chains 71 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 ASN C 111 ASN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.062991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045280 restraints weight = 43156.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047019 restraints weight = 20427.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048192 restraints weight = 12538.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048983 restraints weight = 8929.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049536 restraints weight = 7037.052| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10356 Z= 0.130 Angle : 0.562 11.327 13988 Z= 0.284 Chirality : 0.040 0.151 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.175 126.948 1386 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.46 % Allowed : 9.70 % Favored : 89.83 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1236 helix: 1.93 (0.22), residues: 607 sheet: 0.62 (0.39), residues: 164 loop : 0.26 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 791 TYR 0.010 0.001 TYR A 490 PHE 0.017 0.001 PHE C 255 TRP 0.025 0.001 TRP A 484 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10354) covalent geometry : angle 0.56245 / 0.28 (13982) hydrogen bonds : bond 0.03368 / 2.20 ( 529) hydrogen bonds : angle 4.33081 / 3.10 ( 1482) link_TRANS : bond 0.00131 / 0.07 ( 2) link_TRANS : angle 0.43967 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8083 (m110) cc_final: 0.7832 (m-40) REVERT: B 73 MET cc_start: 0.7276 (tmm) cc_final: 0.7033 (tmm) REVERT: B 110 ARG cc_start: 0.9097 (mtt-85) cc_final: 0.8738 (mmt90) REVERT: A 310 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8598 (mp-120) REVERT: A 364 MET cc_start: 0.9099 (mmt) cc_final: 0.8847 (mmm) REVERT: A 511 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8262 (tm-30) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.0948 time to fit residues: 10.4103 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 5.9990 chunk 43 optimal weight: 0.0470 chunk 117 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN C 111 ASN C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.062577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.044849 restraints weight = 43097.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046561 restraints weight = 20401.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047730 restraints weight = 12593.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048495 restraints weight = 9046.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049041 restraints weight = 7169.396| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10356 Z= 0.140 Angle : 0.559 11.151 13988 Z= 0.282 Chirality : 0.040 0.151 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.059 121.877 1386 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.55 % Allowed : 10.35 % Favored : 89.09 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1236 helix: 1.96 (0.22), residues: 608 sheet: 0.64 (0.39), residues: 164 loop : 0.26 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 792 TYR 0.012 0.001 TYR A 787 PHE 0.017 0.001 PHE C 255 TRP 0.034 0.001 TRP A 484 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10354) covalent geometry : angle 0.55922 / 0.28 (13982) hydrogen bonds : bond 0.03359 / 2.18 ( 529) hydrogen bonds : angle 4.29654 / 3.08 ( 1482) link_TRANS : bond 0.00129 / 0.06 ( 2) link_TRANS : angle 0.40897 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8162 (m110) cc_final: 0.7940 (m-40) REVERT: B 110 ARG cc_start: 0.9139 (mtt-85) cc_final: 0.8769 (mmt90) REVERT: B 120 MET cc_start: 0.7505 (mmm) cc_final: 0.7224 (mpp) REVERT: A 310 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8601 (mp-120) REVERT: A 364 MET cc_start: 0.9077 (mmt) cc_final: 0.8773 (mmm) REVERT: A 478 MET cc_start: 0.7555 (mmm) cc_final: 0.7349 (mmt) REVERT: A 511 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8307 (tm-30) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.0869 time to fit residues: 9.5811 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 116 optimal weight: 0.4980 chunk 70 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.063135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045475 restraints weight = 42995.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.047222 restraints weight = 20173.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048397 restraints weight = 12354.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049194 restraints weight = 8820.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049701 restraints weight = 6940.522| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10356 Z= 0.108 Angle : 0.562 11.763 13988 Z= 0.277 Chirality : 0.040 0.151 1528 Planarity : 0.004 0.051 1789 Dihedral : 6.896 116.640 1386 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.55 % Allowed : 10.63 % Favored : 88.82 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1236 helix: 1.94 (0.22), residues: 613 sheet: 0.65 (0.39), residues: 164 loop : 0.23 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 773 TYR 0.022 0.001 TYR A 490 PHE 0.026 0.001 PHE A 553 TRP 0.040 0.001 TRP A 484 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10354) covalent geometry : angle 0.56156 / 0.28 (13982) hydrogen bonds : bond 0.03193 / 2.07 ( 529) hydrogen bonds : angle 4.20925 / 3.02 ( 1482) link_TRANS : bond 0.00154 / 0.08 ( 2) link_TRANS : angle 0.43546 / 0.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8162 (m110) cc_final: 0.7954 (m-40) REVERT: B 110 ARG cc_start: 0.9144 (mtt-85) cc_final: 0.8773 (mmt90) REVERT: B 120 MET cc_start: 0.7481 (mmm) cc_final: 0.7251 (mpp) REVERT: A 310 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8595 (mp-120) REVERT: A 364 MET cc_start: 0.9092 (mmt) cc_final: 0.8782 (mmm) REVERT: A 511 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8320 (tm-30) REVERT: C 227 MET cc_start: 0.8824 (ttm) cc_final: 0.8515 (tpp) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.0859 time to fit residues: 10.1860 Evaluate side-chains 78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN C 111 ASN C 121 GLN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.043893 restraints weight = 43155.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045561 restraints weight = 20591.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046693 restraints weight = 12804.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047469 restraints weight = 9198.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047972 restraints weight = 7296.739| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10356 Z= 0.185 Angle : 0.620 11.056 13988 Z= 0.307 Chirality : 0.041 0.163 1528 Planarity : 0.004 0.049 1789 Dihedral : 6.937 115.502 1386 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.65 % Allowed : 10.63 % Favored : 88.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1236 helix: 1.91 (0.22), residues: 613 sheet: 0.61 (0.38), residues: 164 loop : 0.11 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 789 TYR 0.013 0.001 TYR A 259 PHE 0.019 0.002 PHE C 255 TRP 0.012 0.001 TRP C 79 HIS 0.008 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (10354) covalent geometry : angle 0.62021 / 0.31 (13982) hydrogen bonds : bond 0.03593 / 2.33 ( 529) hydrogen bonds : angle 4.34620 / 3.12 ( 1482) link_TRANS : bond 0.00206 / 0.10 ( 2) link_TRANS : angle 0.35269 / 0.24 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8202 (m110) cc_final: 0.8001 (m-40) REVERT: B 110 ARG cc_start: 0.9153 (mtt-85) cc_final: 0.8787 (mmt90) REVERT: A 310 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8562 (mp-120) REVERT: A 364 MET cc_start: 0.9091 (mmt) cc_final: 0.8816 (mmm) REVERT: A 511 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 12 ASN cc_start: 0.8134 (t0) cc_final: 0.7877 (t0) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.0835 time to fit residues: 9.1445 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.062834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.045096 restraints weight = 43094.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046810 restraints weight = 20324.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047968 restraints weight = 12558.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048721 restraints weight = 8972.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049286 restraints weight = 7128.492| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10356 Z= 0.110 Angle : 0.582 10.749 13988 Z= 0.288 Chirality : 0.040 0.152 1528 Planarity : 0.004 0.051 1789 Dihedral : 6.776 114.808 1386 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.46 % Allowed : 11.00 % Favored : 88.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1236 helix: 1.96 (0.22), residues: 613 sheet: 0.60 (0.39), residues: 164 loop : 0.19 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 773 TYR 0.008 0.001 TYR A 102 PHE 0.026 0.001 PHE A 553 TRP 0.036 0.002 TRP A 484 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10354) covalent geometry : angle 0.58255 / 0.29 (13982) hydrogen bonds : bond 0.03263 / 2.09 ( 529) hydrogen bonds : angle 4.20489 / 3.01 ( 1482) link_TRANS : bond 0.00175 / 0.09 ( 2) link_TRANS : angle 0.38436 / 0.24 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.50 seconds wall clock time: 30 minutes 27.52 seconds (1827.52 seconds total)