Starting phenix.real_space_refine on Sun Dec 29 11:54:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plw_13504/12_2024/7plw_13504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plw_13504/12_2024/7plw_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_13504/12_2024/7plw_13504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plw_13504/12_2024/7plw_13504.map" model { file = "/net/cci-nas-00/data/ceres_data/7plw_13504/12_2024/7plw_13504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plw_13504/12_2024/7plw_13504.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 7.04, per 1000 atoms: 0.69 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.28 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: 3.67 Time building geometry restraints manager: 3.25 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: 1.320 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 10354 Z= 0.327 Angle : 0.841 12.259 13982 Z= 0.499 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (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 TRP 0.025 0.003 TRP C 356 HIS 0.011 0.002 HIS A 418 PHE 0.037 0.003 PHE A 564 TYR 0.075 0.006 TYR A 113 ARG 0.093 0.011 ARG C 196 *********************** 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 : 1.257 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: 0.2993 time to fit residues: 61.3635 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 : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN C 128 ASN C 162 ASN C 280 ASN C 296 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10354 Z= 0.212 Angle : 0.647 7.189 13982 Z= 0.345 Chirality : 0.043 0.225 1528 Planarity : 0.005 0.057 1789 Dihedral : 9.562 148.949 1396 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.02 % Allowed : 4.25 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1236 helix: 0.59 (0.20), residues: 613 sheet: 0.81 (0.39), residues: 156 loop : 0.13 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 484 HIS 0.008 0.001 HIS C 275 PHE 0.025 0.002 PHE C 255 TYR 0.029 0.001 TYR A 113 ARG 0.005 0.001 ARG C 372 *********************** 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 107 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8853 (mtp) cc_final: 0.8460 (mmm) REVERT: B 45 ASN cc_start: 0.8265 (m-40) cc_final: 0.8003 (m-40) REVERT: B 110 ARG cc_start: 0.9024 (mtt-85) cc_final: 0.8579 (mtt-85) REVERT: A 203 MET cc_start: 0.8779 (mmm) cc_final: 0.8557 (mmm) REVERT: A 478 MET cc_start: 0.8139 (mmt) cc_final: 0.7878 (mmt) REVERT: A 490 TYR cc_start: 0.6815 (t80) cc_final: 0.6609 (t80) outliers start: 11 outliers final: 4 residues processed: 105 average time/residue: 0.2266 time to fit residues: 35.0465 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 HIS ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10354 Z= 0.210 Angle : 0.586 7.328 13982 Z= 0.307 Chirality : 0.041 0.162 1528 Planarity : 0.004 0.055 1789 Dihedral : 8.992 144.492 1396 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.83 % Allowed : 6.28 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1236 helix: 1.17 (0.21), residues: 615 sheet: 0.76 (0.38), residues: 158 loop : 0.19 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 484 HIS 0.008 0.001 HIS C 275 PHE 0.025 0.002 PHE B 12 TYR 0.012 0.001 TYR A 113 ARG 0.003 0.000 ARG A 278 *********************** 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: 9 poor density : 81 time to evaluate : 1.249 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: 0.8038 (m-40) cc_final: 0.7744 (m-40) REVERT: B 73 MET cc_start: 0.7690 (tmm) cc_final: 0.7379 (tmm) REVERT: B 110 ARG cc_start: 0.8979 (mtt-85) cc_final: 0.8758 (mtt-85) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.2368 time to fit residues: 31.2145 Evaluate side-chains 78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 354 HIS 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 111 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.0270 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10354 Z= 0.186 Angle : 0.564 10.577 13982 Z= 0.290 Chirality : 0.041 0.163 1528 Planarity : 0.004 0.047 1789 Dihedral : 8.635 142.828 1396 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.29 % Allowed : 6.56 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1236 helix: 1.46 (0.21), residues: 613 sheet: 0.62 (0.38), residues: 160 loop : 0.29 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 484 HIS 0.011 0.001 HIS B 147 PHE 0.032 0.001 PHE B 12 TYR 0.010 0.001 TYR A 259 ARG 0.002 0.000 ARG A 692 *********************** 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: 14 poor density : 74 time to evaluate : 1.290 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: 0.8069 (m-40) cc_final: 0.7777 (m-40) REVERT: A 239 MET cc_start: 0.7506 (ttt) cc_final: 0.7231 (ttt) REVERT: A 478 MET cc_start: 0.8173 (mmm) cc_final: 0.7702 (mmt) outliers start: 14 outliers final: 5 residues processed: 86 average time/residue: 0.2162 time to fit residues: 27.7159 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 354 HIS 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 99 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 162 ASN C 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10354 Z= 0.323 Angle : 0.626 10.203 13982 Z= 0.323 Chirality : 0.043 0.191 1528 Planarity : 0.004 0.049 1789 Dihedral : 8.553 138.653 1396 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.20 % Allowed : 8.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1236 helix: 1.52 (0.22), residues: 609 sheet: 0.37 (0.37), residues: 168 loop : 0.16 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 484 HIS 0.011 0.002 HIS B 111 PHE 0.028 0.002 PHE B 12 TYR 0.015 0.001 TYR A 259 ARG 0.003 0.000 ARG B 110 *********************** 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 78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8005 (m-40) cc_final: 0.7724 (m-40) REVERT: B 73 MET cc_start: 0.7472 (tmm) cc_final: 0.6996 (tmm) REVERT: B 110 ARG cc_start: 0.9062 (mtt-85) cc_final: 0.8599 (mmt180) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.2531 time to fit residues: 27.7543 Evaluate side-chains 70 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.0060 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 225 ASN C 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10354 Z= 0.155 Angle : 0.559 10.867 13982 Z= 0.285 Chirality : 0.041 0.172 1528 Planarity : 0.004 0.053 1789 Dihedral : 8.242 129.482 1396 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.83 % Allowed : 9.33 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1236 helix: 1.75 (0.22), residues: 607 sheet: 0.48 (0.38), residues: 166 loop : 0.23 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.023 0.001 PHE B 12 TYR 0.010 0.001 TYR A 7 ARG 0.004 0.000 ARG B 110 *********************** 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 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.272 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: 0.7974 (m110) cc_final: 0.7724 (m-40) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 0.2356 time to fit residues: 29.1578 Evaluate side-chains 69 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10354 Z= 0.168 Angle : 0.578 12.516 13982 Z= 0.289 Chirality : 0.040 0.169 1528 Planarity : 0.004 0.051 1789 Dihedral : 8.007 125.410 1396 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.46 % Allowed : 10.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1236 helix: 1.84 (0.22), residues: 606 sheet: 0.50 (0.39), residues: 166 loop : 0.21 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.027 0.001 PHE B 12 TYR 0.008 0.001 TYR A 490 ARG 0.005 0.000 ARG A 791 *********************** 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 80 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 1.678 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: 0.7987 (m110) cc_final: 0.7747 (m-40) REVERT: A 788 MET cc_start: 0.8698 (mpp) cc_final: 0.8484 (mpp) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.2495 time to fit residues: 29.2535 Evaluate side-chains 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10354 Z= 0.181 Angle : 0.565 9.089 13982 Z= 0.284 Chirality : 0.040 0.169 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.888 120.179 1396 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.65 % Allowed : 10.91 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1236 helix: 1.84 (0.22), residues: 612 sheet: 0.52 (0.39), residues: 166 loop : 0.18 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 484 HIS 0.007 0.001 HIS A 81 PHE 0.028 0.001 PHE B 12 TYR 0.009 0.001 TYR A 490 ARG 0.005 0.000 ARG A 791 *********************** 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: 7 poor density : 70 time to evaluate : 1.244 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: 0.7988 (m110) cc_final: 0.7761 (m-40) REVERT: A 788 MET cc_start: 0.8665 (mpp) cc_final: 0.8324 (mpp) outliers start: 7 outliers final: 7 residues processed: 76 average time/residue: 0.2323 time to fit residues: 26.1606 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 : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 354 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 192 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10354 Z= 0.174 Angle : 0.567 9.236 13982 Z= 0.284 Chirality : 0.040 0.169 1528 Planarity : 0.004 0.051 1789 Dihedral : 7.782 115.578 1396 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.74 % Allowed : 10.72 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1236 helix: 1.84 (0.22), residues: 614 sheet: 0.57 (0.39), residues: 164 loop : 0.19 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 484 HIS 0.008 0.001 HIS A 81 PHE 0.027 0.001 PHE B 12 TYR 0.010 0.001 TYR A 490 ARG 0.004 0.000 ARG A 791 *********************** 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 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.230 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: 0.8000 (m110) cc_final: 0.7777 (m-40) REVERT: A 478 MET cc_start: 0.8372 (mmp) cc_final: 0.8168 (mmp) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.2354 time to fit residues: 27.3379 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 : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 354 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 192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.0070 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 75 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.1490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10354 Z= 0.135 Angle : 0.562 10.179 13982 Z= 0.281 Chirality : 0.040 0.166 1528 Planarity : 0.004 0.052 1789 Dihedral : 7.524 112.838 1396 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.65 % Allowed : 11.00 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1236 helix: 1.68 (0.21), residues: 625 sheet: 0.58 (0.39), residues: 164 loop : 0.14 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 484 HIS 0.007 0.001 HIS A 81 PHE 0.026 0.001 PHE A 553 TYR 0.012 0.001 TYR A 102 ARG 0.002 0.000 ARG A 692 ********************** 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 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.324 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: 0.7986 (m110) cc_final: 0.7781 (m-40) REVERT: A 364 MET cc_start: 0.8034 (mmp) cc_final: 0.7671 (mmm) REVERT: A 478 MET cc_start: 0.8353 (mmp) cc_final: 0.8147 (mmp) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.2330 time to fit residues: 27.6421 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 : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.062409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.044700 restraints weight = 42938.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046416 restraints weight = 20426.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047538 restraints weight = 12660.697| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10354 Z= 0.231 Angle : 0.589 10.118 13982 Z= 0.294 Chirality : 0.041 0.168 1528 Planarity : 0.004 0.049 1789 Dihedral : 7.604 109.575 1396 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.55 % Allowed : 11.37 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1236 helix: 1.78 (0.22), residues: 624 sheet: 0.59 (0.39), residues: 164 loop : 0.07 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.008 0.001 HIS A 418 PHE 0.026 0.001 PHE B 12 TYR 0.011 0.001 TYR A 259 ARG 0.002 0.000 ARG A 773 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.03 seconds wall clock time: 39 minutes 59.12 seconds (2399.12 seconds total)