Starting phenix.real_space_refine on Wed Mar 4 03:25:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plw_13504/03_2026/7plw_13504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plw_13504/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7plw_13504/03_2026/7plw_13504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plw_13504/03_2026/7plw_13504.map" model { file = "/net/cci-nas-00/data/ceres_data/7plw_13504/03_2026/7plw_13504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plw_13504/03_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-5986/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 2.29, per 1000 atoms: 0.23 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: 0.88 Conformation dependent library (CDL) restraints added in 443.2 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: 0.27 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: 6084 30.36 - 60.71: 127 60.71 - 91.07: 40 91.07 - 121.43: 0 121.43 - 151.78: 3 Dihedral angle restraints: 6254 sinusoidal: 2564 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 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1078 0.048 - 0.096: 345 0.096 - 0.144: 93 0.144 - 0.192: 9 0.192 - 0.239: 3 Chirality restraints: 1528 Sorted by residual: 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 chirality pdb=" CA PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.050 0.239 1528 Planarity : 0.008 0.116 1789 Dihedral : 15.159 151.783 3870 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 covalent geometry : bond 0.00505 (10354) covalent geometry : angle 0.84104 (13982) hydrogen bonds : bond 0.16410 ( 529) hydrogen bonds : angle 7.21152 ( 1482) link_TRANS : bond 0.00819 ( 2) link_TRANS : angle 3.99825 ( 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 : 0.322 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: 0.8263 (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: 0.8448 (tpp80) REVERT: A 478 MET cc_start: 0.8209 (mmt) cc_final: 0.7546 (mmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1239 time to fit residues: 25.3069 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 : 0.368 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3422 r_free = 0.3422 target = 0.063819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.045970 restraints weight = 43323.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047760 restraints weight = 20506.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048953 restraints weight = 12520.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049760 restraints weight = 8872.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050337 restraints weight = 6933.758| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10356 Z= 0.142 Angle : 0.639 7.302 13988 Z= 0.341 Chirality : 0.043 0.218 1528 Planarity : 0.005 0.059 1789 Dihedral : 9.535 147.620 1396 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.83 % Allowed : 4.71 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.23), residues: 1236 helix: 0.62 (0.20), residues: 614 sheet: 0.85 (0.39), residues: 154 loop : 0.13 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 372 TYR 0.028 0.001 TYR A 113 PHE 0.025 0.002 PHE B 12 TRP 0.024 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00313 (10354) covalent geometry : angle 0.63931 (13982) hydrogen bonds : bond 0.04311 ( 529) hydrogen bonds : angle 5.04303 ( 1482) link_TRANS : bond 0.00235 ( 2) link_TRANS : angle 0.96141 ( 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 105 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.391 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: 0.8391 (m-40) cc_final: 0.8165 (m-40) REVERT: B 110 ARG cc_start: 0.9167 (mtt-85) cc_final: 0.8720 (mtt-85) REVERT: A 113 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8488 (t80) REVERT: A 478 MET cc_start: 0.8728 (mmt) cc_final: 0.8107 (mmt) REVERT: A 511 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.0881 time to fit residues: 13.6137 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 : 0.424 ------------------------------------------------------------------------------- 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: 0.5980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.045669 restraints weight = 43282.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047433 restraints weight = 20477.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048619 restraints weight = 12526.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049415 restraints weight = 8903.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049926 restraints weight = 6983.777| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2848 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= 0.129 Angle : 0.570 6.697 13988 Z= 0.298 Chirality : 0.041 0.157 1528 Planarity : 0.004 0.055 1789 Dihedral : 8.881 146.576 1396 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.02 % Allowed : 5.73 % Favored : 93.25 % 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: 1.10 (0.24), residues: 1236 helix: 1.22 (0.21), residues: 617 sheet: 0.65 (0.38), residues: 160 loop : 0.25 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.017 0.001 TYR A 113 PHE 0.022 0.002 PHE B 12 TRP 0.032 0.002 TRP A 484 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00288 (10354) covalent geometry : angle 0.56954 (13982) hydrogen bonds : bond 0.03791 ( 529) hydrogen bonds : angle 4.74477 ( 1482) link_TRANS : bond 0.00190 ( 2) link_TRANS : angle 0.92374 ( 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 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8880 (mtp) cc_final: 0.8384 (mmm) REVERT: B 45 ASN cc_start: 0.8249 (m-40) cc_final: 0.8003 (m-40) REVERT: A 478 MET cc_start: 0.8656 (mmt) cc_final: 0.7889 (mmm) REVERT: A 511 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 44 MET cc_start: 0.8490 (mtp) cc_final: 0.8228 (ttm) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 0.0894 time to fit residues: 11.4613 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 : 0.398 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 HIS ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN C 121 GLN C 162 ASN C 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.044734 restraints weight = 43574.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046467 restraints weight = 20591.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047623 restraints weight = 12634.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048399 restraints weight = 9044.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048829 restraints weight = 7130.805| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10356 Z= 0.155 Angle : 0.575 9.778 13988 Z= 0.298 Chirality : 0.041 0.162 1528 Planarity : 0.004 0.046 1789 Dihedral : 8.585 142.525 1396 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.92 % Allowed : 7.02 % Favored : 92.05 % 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: 1.25 (0.24), residues: 1236 helix: 1.44 (0.21), residues: 614 sheet: 0.62 (0.38), residues: 162 loop : 0.21 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 110 TYR 0.014 0.001 TYR A 113 PHE 0.031 0.002 PHE B 12 TRP 0.040 0.002 TRP A 484 HIS 0.008 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00353 (10354) covalent geometry : angle 0.57443 (13982) hydrogen bonds : bond 0.03703 ( 529) hydrogen bonds : angle 4.66898 ( 1482) link_TRANS : bond 0.00035 ( 2) link_TRANS : angle 0.82818 ( 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 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.403 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: 0.8200 (m-40) cc_final: 0.7968 (m-40) REVERT: B 110 ARG cc_start: 0.9140 (mtt-85) cc_final: 0.8852 (mmt180) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.0971 time to fit residues: 11.0459 Evaluate side-chains 67 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 106 THR 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: 2.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS A 418 HIS A 680 GLN C 111 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 = 0.3404 r_free = 0.3404 target = 0.063035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045269 restraints weight = 42999.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047024 restraints weight = 20241.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048191 restraints weight = 12418.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048976 restraints weight = 8854.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049500 restraints weight = 6990.644| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.117 Angle : 0.549 10.371 13988 Z= 0.282 Chirality : 0.041 0.163 1528 Planarity : 0.004 0.050 1789 Dihedral : 8.309 137.305 1396 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.92 % Allowed : 8.60 % Favored : 90.48 % 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: 1.44 (0.24), residues: 1236 helix: 1.69 (0.22), residues: 603 sheet: 0.49 (0.38), residues: 168 loop : 0.29 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 110 TYR 0.009 0.001 TYR A 259 PHE 0.026 0.001 PHE B 12 TRP 0.033 0.001 TRP A 484 HIS 0.009 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00263 (10354) covalent geometry : angle 0.54847 (13982) hydrogen bonds : bond 0.03460 ( 529) hydrogen bonds : angle 4.47511 ( 1482) link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.85242 ( 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 77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.426 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: 0.8231 (m-40) cc_final: 0.7962 (m-40) REVERT: B 110 ARG cc_start: 0.9154 (mtt-85) cc_final: 0.8878 (mmt180) REVERT: A 478 MET cc_start: 0.7644 (mmm) cc_final: 0.6276 (mmt) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.0929 time to fit residues: 10.4475 Evaluate side-chains 68 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL 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: 2.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.0370 chunk 24 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3414 r_free = 0.3414 target = 0.063395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045611 restraints weight = 43247.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047387 restraints weight = 20296.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048580 restraints weight = 12377.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049347 restraints weight = 8788.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049915 restraints weight = 6931.554| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10356 Z= 0.106 Angle : 0.535 10.338 13988 Z= 0.273 Chirality : 0.040 0.164 1528 Planarity : 0.004 0.052 1789 Dihedral : 8.083 131.147 1396 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.92 % Allowed : 8.96 % Favored : 90.11 % 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: 1.56 (0.24), residues: 1236 helix: 1.83 (0.22), residues: 602 sheet: 0.53 (0.38), residues: 166 loop : 0.30 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 110 TYR 0.012 0.001 TYR A 490 PHE 0.022 0.001 PHE B 12 TRP 0.054 0.002 TRP A 484 HIS 0.018 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00238 (10354) covalent geometry : angle 0.53522 (13982) hydrogen bonds : bond 0.03352 ( 529) hydrogen bonds : angle 4.34093 ( 1482) link_TRANS : bond 0.00136 ( 2) link_TRANS : angle 0.86217 ( 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 78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.376 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: 0.8140 (m110) cc_final: 0.7902 (m-40) REVERT: B 110 ARG cc_start: 0.9157 (mtt-85) cc_final: 0.8899 (mmt180) REVERT: A 418 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8594 (m-70) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.0967 time to fit residues: 10.9653 Evaluate side-chains 69 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS 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 111 ASN Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS 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 = 0.3403 r_free = 0.3403 target = 0.062853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045283 restraints weight = 42866.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046982 restraints weight = 20452.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048148 restraints weight = 12644.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048925 restraints weight = 9059.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049450 restraints weight = 7147.407| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3752 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= 0.121 Angle : 0.548 12.807 13988 Z= 0.276 Chirality : 0.040 0.163 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.935 126.600 1396 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.74 % Allowed : 9.52 % Favored : 89.74 % 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: 1.60 (0.24), residues: 1236 helix: 1.90 (0.22), residues: 602 sheet: 0.50 (0.39), residues: 166 loop : 0.27 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 791 TYR 0.008 0.001 TYR A 259 PHE 0.020 0.001 PHE B 12 TRP 0.021 0.001 TRP A 484 HIS 0.006 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00278 (10354) covalent geometry : angle 0.54804 (13982) hydrogen bonds : bond 0.03322 ( 529) hydrogen bonds : angle 4.29716 ( 1482) link_TRANS : bond 0.00079 ( 2) link_TRANS : angle 0.82838 ( 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 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 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: 0.8116 (m110) cc_final: 0.7886 (m-40) REVERT: B 110 ARG cc_start: 0.9129 (mtt-85) cc_final: 0.8915 (mmt180) REVERT: A 364 MET cc_start: 0.8998 (mmp) cc_final: 0.8777 (mmt) REVERT: A 788 MET cc_start: 0.8869 (mpp) cc_final: 0.8600 (mpp) REVERT: C 292 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7370 (p0) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.0809 time to fit residues: 8.9725 Evaluate side-chains 69 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS 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 111 ASN Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.062892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045307 restraints weight = 42821.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047036 restraints weight = 20117.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048198 restraints weight = 12377.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048972 restraints weight = 8857.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049528 restraints weight = 6974.207| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3861 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= 0.115 Angle : 0.561 10.130 13988 Z= 0.277 Chirality : 0.040 0.163 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.801 121.949 1396 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.55 % Allowed : 10.17 % Favored : 89.28 % 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: 1.63 (0.24), residues: 1236 helix: 1.94 (0.22), residues: 607 sheet: 0.52 (0.39), residues: 166 loop : 0.25 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 791 TYR 0.014 0.001 TYR A 490 PHE 0.034 0.001 PHE B 12 TRP 0.022 0.001 TRP A 484 HIS 0.016 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00262 (10354) covalent geometry : angle 0.56106 (13982) hydrogen bonds : bond 0.03262 ( 529) hydrogen bonds : angle 4.24410 ( 1482) link_TRANS : bond 0.00096 ( 2) link_TRANS : angle 0.82743 ( 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 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.259 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: 0.8122 (m110) cc_final: 0.7907 (m-40) REVERT: B 110 ARG cc_start: 0.9103 (mtt-85) cc_final: 0.8888 (mmt180) REVERT: A 788 MET cc_start: 0.8871 (mpp) cc_final: 0.8499 (mpp) REVERT: C 227 MET cc_start: 0.8855 (ttm) cc_final: 0.8576 (tpp) REVERT: C 292 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7380 (p0) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.0878 time to fit residues: 9.2621 Evaluate side-chains 68 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 292 ASP 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: 0.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 0.0970 chunk 120 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045828 restraints weight = 42923.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.047563 restraints weight = 20422.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048743 restraints weight = 12588.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049551 restraints weight = 9020.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050090 restraints weight = 7060.975| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10356 Z= 0.099 Angle : 0.557 10.786 13988 Z= 0.272 Chirality : 0.040 0.162 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.574 113.851 1396 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.55 % Allowed : 9.89 % Favored : 89.56 % 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: 1.66 (0.24), residues: 1236 helix: 1.92 (0.22), residues: 612 sheet: 0.59 (0.39), residues: 164 loop : 0.29 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 791 TYR 0.007 0.001 TYR A 102 PHE 0.033 0.001 PHE B 12 TRP 0.042 0.001 TRP A 484 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00227 (10354) covalent geometry : angle 0.55661 (13982) hydrogen bonds : bond 0.03057 ( 529) hydrogen bonds : angle 4.13460 ( 1482) link_TRANS : bond 0.00152 ( 2) link_TRANS : angle 0.83083 ( 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 78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.358 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: 0.8172 (m110) cc_final: 0.7971 (m-40) REVERT: B 110 ARG cc_start: 0.9124 (mtt-85) cc_final: 0.8905 (mmt180) REVERT: C 227 MET cc_start: 0.8821 (ttm) cc_final: 0.8537 (tpp) REVERT: C 292 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7334 (p0) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.1042 time to fit residues: 11.6781 Evaluate side-chains 70 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.062955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045245 restraints weight = 42841.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046974 restraints weight = 20393.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048116 restraints weight = 12628.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048930 restraints weight = 9071.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049476 restraints weight = 7125.568| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.126 Angle : 0.564 10.651 13988 Z= 0.278 Chirality : 0.040 0.163 1528 Planarity : 0.004 0.050 1789 Dihedral : 7.509 111.249 1396 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.55 % Allowed : 10.44 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.65 (0.24), residues: 1236 helix: 1.91 (0.22), residues: 613 sheet: 0.60 (0.39), residues: 164 loop : 0.26 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 792 TYR 0.016 0.001 TYR A 490 PHE 0.032 0.001 PHE B 12 TRP 0.031 0.001 TRP A 484 HIS 0.008 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00289 (10354) covalent geometry : angle 0.56394 (13982) hydrogen bonds : bond 0.03171 ( 529) hydrogen bonds : angle 4.17255 ( 1482) link_TRANS : bond 0.00054 ( 2) link_TRANS : angle 0.80495 ( 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 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9136 (mtt-85) cc_final: 0.8914 (mmt180) REVERT: C 227 MET cc_start: 0.8849 (ttm) cc_final: 0.8549 (tpp) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.1023 time to fit residues: 10.7946 Evaluate side-chains 69 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045502 restraints weight = 43094.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047228 restraints weight = 20484.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048398 restraints weight = 12690.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049209 restraints weight = 9049.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049737 restraints weight = 7107.207| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.113 Angle : 0.567 10.825 13988 Z= 0.280 Chirality : 0.040 0.163 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.471 109.945 1396 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.55 % Allowed : 10.35 % Favored : 89.09 % 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: 1.68 (0.24), residues: 1236 helix: 1.96 (0.22), residues: 612 sheet: 0.61 (0.39), residues: 164 loop : 0.25 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 290 TYR 0.009 0.001 TYR A 787 PHE 0.031 0.001 PHE B 12 TRP 0.046 0.002 TRP A 484 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00259 (10354) covalent geometry : angle 0.56686 (13982) hydrogen bonds : bond 0.03104 ( 529) hydrogen bonds : angle 4.13527 ( 1482) link_TRANS : bond 0.00097 ( 2) link_TRANS : angle 0.81883 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.63 seconds wall clock time: 32 minutes 10.02 seconds (1930.02 seconds total)