Starting phenix.real_space_refine on Wed Mar 4 03:25:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plx_13505/03_2026/7plx_13505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plx_13505/03_2026/7plx_13505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7plx_13505/03_2026/7plx_13505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plx_13505/03_2026/7plx_13505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plx_13505/03_2026/7plx_13505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plx_13505/03_2026/7plx_13505.map" } resolution = 3.6 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 40 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: 1.70, per 1000 atoms: 0.17 Number of scatterers: 10139 At special positions: 0 Unit cell: (102.82, 136.74, 150.52, 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: 0.86 Conformation dependent library (CDL) restraints added in 440.9 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: 64 helices and 14 sheets defined 56.5% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.023A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.522A 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 73 through 77 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.539A pdb=" N ARG A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.222A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.647A pdb=" N SER A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.883A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.619A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.501A 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 185 removed outlier: 3.539A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.597A 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 267 removed outlier: 4.182A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.877A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.658A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.052A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.567A pdb=" N MET A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.697A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.953A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.636A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.912A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 removed outlier: 3.583A pdb=" N HIS A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.574A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.613A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.751A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.664A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.052A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 4.492A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.717A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.582A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.930A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.629A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.724A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.949A 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: 4.553A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.585A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.801A 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 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.053A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.896A 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 211 removed outlier: 6.372A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.324A 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: 3.580A 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: 4.460A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (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: 6.282A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 527 hydrogen bonds defined for protein. 1446 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: 1.42 Time building geometry restraints manager: 1.10 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 3.53e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.200 0.063 2.00e-02 2.50e+03 1.00e+01 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 7.84e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.31e+00 ... (remaining 10349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 13739 2.50 - 4.99: 215 4.99 - 7.49: 18 7.49 - 9.98: 7 9.98 - 12.48: 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 121.70 110.99 10.71 1.80e+00 3.09e-01 3.54e+01 angle pdb=" N TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.50 102.55 7.95 1.70e+00 3.46e-01 2.18e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 101.62 8.48 1.90e+00 2.77e-01 1.99e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.86 -4.86 1.10e+00 8.26e-01 1.95e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.18 4.22 1.00e+00 1.00e+00 1.78e+01 ... (remaining 13977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 6097 30.52 - 61.04: 115 61.04 - 91.56: 39 91.56 - 122.08: 1 122.08 - 152.60: 2 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 92.60 -152.60 1 2.00e+01 2.50e-03 4.53e+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 82.51 -142.51 1 2.00e+01 2.50e-03 4.30e+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 300.00 178.43 121.57 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1030 0.042 - 0.084: 345 0.084 - 0.127: 126 0.127 - 0.169: 21 0.169 - 0.211: 6 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 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 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 2.71 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA TYR A 175 " pdb=" N TYR A 175 " pdb=" C TYR A 175 " pdb=" CB TYR A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1525 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 12 " -0.299 9.50e-02 1.11e+02 1.38e-01 2.42e+01 pdb=" NE ARG A 12 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 12 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG A 12 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 12 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.103 9.50e-02 1.11e+02 6.01e-02 2.00e+01 pdb=" NE ARG A 278 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 641 " -0.100 9.50e-02 1.11e+02 5.88e-02 1.92e+01 pdb=" NE ARG A 641 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 641 " -0.072 2.00e-02 2.50e+03 pdb=" NH1 ARG A 641 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 641 " 0.021 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 16 2.36 - 3.00: 5439 3.00 - 3.63: 15038 3.63 - 4.27: 22471 4.27 - 4.90: 37956 Nonbonded interactions: 80920 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" OE1 GLU A 144 " pdb=" OH TYR A 179 " model vdw 2.073 3.040 nonbonded pdb=" O THR C 149 " pdb=" ND2 ASN C 296 " model vdw 2.142 3.120 nonbonded pdb=" O TRP H 1 " pdb=" O1 EEP H 2 " model vdw 2.166 3.040 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.176 3.120 ... (remaining 80915 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: 2.260 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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= 0.222 Angle : 0.829 12.478 13988 Z= 0.490 Chirality : 0.049 0.211 1528 Planarity : 0.008 0.138 1789 Dihedral : 14.949 152.600 3870 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1236 helix: -1.39 (0.17), residues: 587 sheet: 0.91 (0.38), residues: 155 loop : -0.28 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.012 ARG A 278 TYR 0.038 0.006 TYR C 306 PHE 0.032 0.002 PHE A 564 TRP 0.036 0.004 TRP C 79 HIS 0.010 0.002 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00463 (10354) covalent geometry : angle 0.82317 (13982) hydrogen bonds : bond 0.15905 ( 525) hydrogen bonds : angle 6.83003 ( 1446) link_TRANS : bond 0.00653 ( 2) link_TRANS : angle 4.73778 ( 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 162 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1247 time to fit residues: 26.8530 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 81 HIS A 87 HIS A 149 GLN A 238 ASN A 264 GLN A 290 GLN A 410 ASN A 463 GLN A 468 HIS A 497 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 HIS ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 775 GLN C 128 ASN C 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.057679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.043304 restraints weight = 51327.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044870 restraints weight = 26720.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045959 restraints weight = 17103.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046715 restraints weight = 12470.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047221 restraints weight = 9884.044| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10356 Z= 0.199 Angle : 0.683 7.599 13988 Z= 0.364 Chirality : 0.044 0.171 1528 Planarity : 0.005 0.053 1789 Dihedral : 9.234 154.824 1396 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.20 % Allowed : 5.91 % 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 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: 0.65 (0.23), residues: 1236 helix: 0.54 (0.20), residues: 609 sheet: 1.13 (0.39), residues: 157 loop : 0.25 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 37 TYR 0.018 0.002 TYR C 279 PHE 0.025 0.002 PHE C 255 TRP 0.026 0.003 TRP C 79 HIS 0.011 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00443 (10354) covalent geometry : angle 0.68235 (13982) hydrogen bonds : bond 0.05011 ( 525) hydrogen bonds : angle 5.10752 ( 1446) link_TRANS : bond 0.00174 ( 2) link_TRANS : angle 1.42978 ( 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 104 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8216 (m-80) cc_final: 0.7999 (m-80) REVERT: A 473 GLU cc_start: 0.8792 (tp30) cc_final: 0.8086 (tp30) REVERT: A 511 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 761 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9122 (tptt) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 0.0876 time to fit residues: 13.0208 Evaluate side-chains 82 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 113 optimal weight: 0.0980 chunk 67 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A 717 GLN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.059184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044800 restraints weight = 50154.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046441 restraints weight = 25635.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047570 restraints weight = 16218.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048375 restraints weight = 11703.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048944 restraints weight = 9185.701| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10356 Z= 0.117 Angle : 0.595 7.091 13988 Z= 0.309 Chirality : 0.042 0.182 1528 Planarity : 0.004 0.057 1789 Dihedral : 8.607 163.991 1396 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.20 % Allowed : 6.84 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.24), residues: 1236 helix: 1.23 (0.21), residues: 609 sheet: 1.62 (0.42), residues: 151 loop : 0.38 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 372 TYR 0.010 0.001 TYR A 127 PHE 0.019 0.001 PHE C 255 TRP 0.014 0.002 TRP A 414 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00248 (10354) covalent geometry : angle 0.59454 (13982) hydrogen bonds : bond 0.03920 ( 525) hydrogen bonds : angle 4.67038 ( 1446) link_TRANS : bond 0.00265 ( 2) link_TRANS : angle 1.28572 ( 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 110 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8256 (m-80) cc_final: 0.8008 (m-80) REVERT: B 36 MET cc_start: 0.9038 (mtt) cc_final: 0.8828 (mtt) REVERT: A 473 GLU cc_start: 0.8904 (tp30) cc_final: 0.8358 (tp30) REVERT: A 511 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 372 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8091 (ttp80) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.0838 time to fit residues: 12.8801 Evaluate side-chains 82 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.058635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.044208 restraints weight = 50583.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045784 restraints weight = 26056.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046898 restraints weight = 16672.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047617 restraints weight = 12080.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048193 restraints weight = 9589.934| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3321 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= 0.121 Angle : 0.573 6.814 13988 Z= 0.294 Chirality : 0.041 0.163 1528 Planarity : 0.004 0.057 1789 Dihedral : 8.286 170.042 1396 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.57 % Allowed : 7.76 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.51 (0.24), residues: 1236 helix: 1.44 (0.21), residues: 605 sheet: 1.48 (0.41), residues: 156 loop : 0.41 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 372 TYR 0.010 0.001 TYR A 259 PHE 0.020 0.001 PHE C 255 TRP 0.012 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00267 (10354) covalent geometry : angle 0.57245 (13982) hydrogen bonds : bond 0.03631 ( 525) hydrogen bonds : angle 4.54160 ( 1446) link_TRANS : bond 0.00089 ( 2) link_TRANS : angle 0.80076 ( 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 95 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8369 (m-80) cc_final: 0.8098 (m-80) REVERT: A 473 GLU cc_start: 0.8878 (tp30) cc_final: 0.8301 (tp30) REVERT: A 511 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 176 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7485 (mpp) outliers start: 17 outliers final: 9 residues processed: 88 average time/residue: 0.0725 time to fit residues: 9.9544 Evaluate side-chains 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 242 LEU 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: 0.9980 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.057378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.043049 restraints weight = 51007.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044593 restraints weight = 26524.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045677 restraints weight = 16991.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.046388 restraints weight = 12375.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046950 restraints weight = 9863.716| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10356 Z= 0.174 Angle : 0.600 9.618 13988 Z= 0.305 Chirality : 0.041 0.149 1528 Planarity : 0.004 0.052 1789 Dihedral : 8.191 178.339 1396 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.29 % Allowed : 8.60 % 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: 1.39 (0.24), residues: 1236 helix: 1.41 (0.21), residues: 620 sheet: 1.29 (0.40), residues: 155 loop : 0.27 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.016 0.001 TYR A 79 PHE 0.019 0.001 PHE C 255 TRP 0.010 0.001 TRP A 414 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00386 (10354) covalent geometry : angle 0.59999 (13982) hydrogen bonds : bond 0.03784 ( 525) hydrogen bonds : angle 4.56149 ( 1446) link_TRANS : bond 0.00089 ( 2) link_TRANS : angle 0.77490 ( 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 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8888 (tp30) cc_final: 0.8113 (tp30) REVERT: A 511 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8458 (tm-30) REVERT: C 176 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7042 (mpp) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.0953 time to fit residues: 11.6195 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 : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 552 HIS ** 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 = 0.3346 r_free = 0.3346 target = 0.058398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043994 restraints weight = 51016.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045560 restraints weight = 26279.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046659 restraints weight = 16829.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047446 restraints weight = 12192.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047958 restraints weight = 9572.597| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10356 Z= 0.110 Angle : 0.561 7.815 13988 Z= 0.284 Chirality : 0.040 0.151 1528 Planarity : 0.004 0.052 1789 Dihedral : 7.624 160.509 1396 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.20 % Allowed : 9.06 % 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: 1.53 (0.24), residues: 1236 helix: 1.61 (0.21), residues: 619 sheet: 1.26 (0.41), residues: 155 loop : 0.23 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 372 TYR 0.013 0.001 TYR A 127 PHE 0.015 0.001 PHE C 255 TRP 0.007 0.001 TRP A 414 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00245 (10354) covalent geometry : angle 0.56130 (13982) hydrogen bonds : bond 0.03383 ( 525) hydrogen bonds : angle 4.41441 ( 1446) link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.80617 ( 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 98 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8881 (tp30) cc_final: 0.8302 (tp30) REVERT: A 511 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 47 MET cc_start: 0.7908 (ppp) cc_final: 0.7705 (ppp) REVERT: C 176 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7341 (mpp) REVERT: C 372 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8082 (ttp80) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.0943 time to fit residues: 13.2865 Evaluate side-chains 91 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 242 LEU 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: 6.9990 chunk 85 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.057243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.043003 restraints weight = 50674.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044539 restraints weight = 26288.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045583 restraints weight = 16839.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046351 restraints weight = 12264.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046841 restraints weight = 9721.159| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10356 Z= 0.160 Angle : 0.585 7.696 13988 Z= 0.296 Chirality : 0.041 0.151 1528 Planarity : 0.004 0.050 1789 Dihedral : 7.006 130.309 1396 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.66 % Allowed : 9.98 % 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 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: 1.50 (0.24), residues: 1236 helix: 1.61 (0.21), residues: 614 sheet: 1.20 (0.40), residues: 155 loop : 0.20 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 372 TYR 0.013 0.001 TYR A 259 PHE 0.016 0.001 PHE C 255 TRP 0.007 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00359 (10354) covalent geometry : angle 0.58519 (13982) hydrogen bonds : bond 0.03606 ( 525) hydrogen bonds : angle 4.48087 ( 1446) link_TRANS : bond 0.00073 ( 2) link_TRANS : angle 0.75506 ( 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 96 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 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 36 MET cc_start: 0.8917 (mtt) cc_final: 0.8672 (mmt) REVERT: A 323 MET cc_start: 0.8928 (mmm) cc_final: 0.8501 (tmm) REVERT: A 473 GLU cc_start: 0.8874 (tp30) cc_final: 0.8124 (tp30) REVERT: A 511 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 47 MET cc_start: 0.7827 (ppp) cc_final: 0.7613 (ppp) REVERT: C 176 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7301 (mpp) outliers start: 18 outliers final: 13 residues processed: 93 average time/residue: 0.0843 time to fit residues: 12.1282 Evaluate side-chains 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 102 optimal weight: 0.0270 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 552 HIS ** 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 = 0.3340 r_free = 0.3340 target = 0.058084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043823 restraints weight = 50317.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.045350 restraints weight = 26069.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046451 restraints weight = 16793.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047225 restraints weight = 12229.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047717 restraints weight = 9617.813| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3983 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 : 0.590 10.544 13988 Z= 0.294 Chirality : 0.040 0.175 1528 Planarity : 0.004 0.054 1789 Dihedral : 6.490 105.142 1396 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.20 % Allowed : 10.54 % Favored : 88.26 % 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: 1.68 (0.21), residues: 617 sheet: 1.07 (0.39), residues: 159 loop : 0.26 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 372 TYR 0.012 0.001 TYR A 127 PHE 0.012 0.001 PHE C 255 TRP 0.007 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00259 (10354) covalent geometry : angle 0.59036 (13982) hydrogen bonds : bond 0.03362 ( 525) hydrogen bonds : angle 4.44484 ( 1446) link_TRANS : bond 0.00103 ( 2) link_TRANS : angle 0.78875 ( 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 95 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 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: A 370 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 473 GLU cc_start: 0.8860 (tp30) cc_final: 0.8283 (tp30) REVERT: A 511 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 515 MET cc_start: 0.8877 (tpt) cc_final: 0.8628 (tpp) REVERT: C 123 MET cc_start: 0.8994 (tpp) cc_final: 0.8776 (mmm) REVERT: C 176 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7296 (mpp) REVERT: C 305 MET cc_start: 0.9401 (mmm) cc_final: 0.8892 (mmm) outliers start: 13 outliers final: 11 residues processed: 91 average time/residue: 0.0890 time to fit residues: 12.6204 Evaluate side-chains 89 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043760 restraints weight = 50541.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045321 restraints weight = 26109.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046412 restraints weight = 16722.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047060 restraints weight = 12117.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.047684 restraints weight = 9730.772| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4101 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= 0.122 Angle : 0.603 10.073 13988 Z= 0.299 Chirality : 0.040 0.170 1528 Planarity : 0.004 0.052 1789 Dihedral : 6.177 87.893 1396 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 10.72 % Favored : 87.99 % 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: 1.61 (0.24), residues: 1236 helix: 1.74 (0.21), residues: 610 sheet: 1.08 (0.40), residues: 159 loop : 0.28 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 372 TYR 0.011 0.001 TYR A 127 PHE 0.012 0.001 PHE C 255 TRP 0.005 0.001 TRP A 414 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00272 (10354) covalent geometry : angle 0.60264 (13982) hydrogen bonds : bond 0.03335 ( 525) hydrogen bonds : angle 4.45328 ( 1446) link_TRANS : bond 0.00073 ( 2) link_TRANS : angle 0.78360 ( 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 95 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8839 (tp30) cc_final: 0.8064 (tp30) REVERT: A 511 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 123 MET cc_start: 0.8998 (tpp) cc_final: 0.8764 (mmm) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.0965 time to fit residues: 13.2096 Evaluate side-chains 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.0770 chunk 18 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 chunk 118 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.058767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044585 restraints weight = 49793.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046148 restraints weight = 25712.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047258 restraints weight = 16461.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047997 restraints weight = 11913.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048576 restraints weight = 9447.132| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10356 Z= 0.108 Angle : 0.637 11.835 13988 Z= 0.314 Chirality : 0.041 0.167 1528 Planarity : 0.004 0.054 1789 Dihedral : 5.895 81.410 1396 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.02 % Allowed : 11.18 % Favored : 87.80 % 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: 1.78 (0.22), residues: 608 sheet: 1.25 (0.40), residues: 160 loop : 0.28 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 372 TYR 0.010 0.001 TYR A 127 PHE 0.012 0.001 PHE C 255 TRP 0.011 0.001 TRP A 374 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00240 (10354) covalent geometry : angle 0.63645 (13982) hydrogen bonds : bond 0.03247 ( 525) hydrogen bonds : angle 4.41357 ( 1446) link_TRANS : bond 0.00151 ( 2) link_TRANS : angle 0.81012 ( 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 99 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.7063 (ptp) cc_final: 0.6056 (ppp) REVERT: A 225 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 473 GLU cc_start: 0.8831 (tp30) cc_final: 0.8456 (tp30) REVERT: A 511 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8611 (tm-30) REVERT: C 123 MET cc_start: 0.8984 (tpp) cc_final: 0.8746 (mmm) REVERT: C 305 MET cc_start: 0.9363 (mmm) cc_final: 0.8863 (mmm) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.0900 time to fit residues: 13.1501 Evaluate side-chains 88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.043176 restraints weight = 51076.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044695 restraints weight = 26302.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045753 restraints weight = 16707.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046433 restraints weight = 12043.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046973 restraints weight = 9545.564| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10356 Z= 0.179 Angle : 0.687 10.373 13988 Z= 0.340 Chirality : 0.043 0.189 1528 Planarity : 0.004 0.053 1789 Dihedral : 5.910 81.057 1396 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.11 % Allowed : 11.46 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.24), residues: 1236 helix: 1.68 (0.21), residues: 608 sheet: 1.10 (0.40), residues: 159 loop : 0.19 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 372 TYR 0.014 0.001 TYR A 259 PHE 0.013 0.001 PHE C 255 TRP 0.007 0.001 TRP A 702 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00397 (10354) covalent geometry : angle 0.68698 (13982) hydrogen bonds : bond 0.03662 ( 525) hydrogen bonds : angle 4.53625 ( 1446) link_TRANS : bond 0.00112 ( 2) link_TRANS : angle 0.76184 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.36 seconds wall clock time: 32 minutes 34.03 seconds (1954.03 seconds total)