Starting phenix.real_space_refine on Thu Jul 2 21:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7plx_13505/07_2026/7plx_13505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plx_13505/07_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_13505/07_2026/7plx_13505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2026/7plx_13505.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2026/7plx_13505.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2026/7plx_13505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2026/7plx_13505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.66, per 1000 atoms: 0.16 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: 0.78 Conformation dependent library (CDL) restraints added in 279.1 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: 0.18 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: 1.32 Time building geometry restraints manager: 1.01 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: 6089 30.52 - 61.04: 113 61.04 - 91.56: 39 91.56 - 122.08: 1 122.08 - 152.60: 2 Dihedral angle restraints: 6244 sinusoidal: 2554 harmonic: 3690 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 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 6241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 1526 1.025 - 2.049: 0 2.049 - 3.074: 0 3.074 - 4.099: 0 4.099 - 5.123: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.57 5.12 2.00e-01 2.50e+01 6.56e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.42 4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" CA GLU A 512 " pdb=" N GLU A 512 " pdb=" C GLU A 512 " pdb=" CB GLU A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.330 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.189 5.123 1528 Planarity : 0.008 0.138 1789 Dihedral : 14.884 152.600 3860 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/Z covalent geometry : bond 0.00463 / 0.22 (10354) covalent geometry : angle 0.82317 / 0.49 (13982) hydrogen bonds : bond 0.15905 / 10.61 ( 525) hydrogen bonds : angle 6.83003 / 4.94 ( 1446) link_TRANS : bond 0.00653 / 0.33 ( 2) link_TRANS : angle 4.73778 / 4.25 ( 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 : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 LEU cc_start: 0.9498 (tp) cc_final: 0.9279 (mt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0915 time to fit residues: 19.9666 Evaluate side-chains 84 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 A 657 HIS ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 775 GLN C 128 ASN C 162 ASN C 280 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.043565 restraints weight = 51006.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045151 restraints weight = 26548.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046256 restraints weight = 17012.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046998 restraints weight = 12404.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047542 restraints weight = 9866.946| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10356 Z= 0.191 Angle : 0.690 7.666 13988 Z= 0.366 Chirality : 0.044 0.174 1528 Planarity : 0.005 0.054 1789 Dihedral : 8.743 155.533 1386 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.20 % Allowed : 6.19 % Favored : 92.61 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1236 helix: 0.60 (0.20), residues: 609 sheet: 1.12 (0.39), residues: 159 loop : 0.29 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.018 0.002 TYR C 279 PHE 0.025 0.002 PHE C 255 TRP 0.024 0.002 TRP C 79 HIS 0.010 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (10354) covalent geometry : angle 0.68943 / 0.37 (13982) hydrogen bonds : bond 0.04737 / 3.04 ( 525) hydrogen bonds : angle 5.04907 / 3.59 ( 1446) link_TRANS : bond 0.00501 / 0.26 ( 2) link_TRANS : angle 1.48024 / 1.27 ( 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 106 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8797 (tp30) cc_final: 0.8074 (tp30) REVERT: A 511 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 761 LYS cc_start: 0.9473 (ttmm) cc_final: 0.9125 (tptt) REVERT: A 783 MET cc_start: 0.9262 (tmm) cc_final: 0.9057 (tmm) outliers start: 13 outliers final: 7 residues processed: 101 average time/residue: 0.0718 time to fit residues: 10.9244 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 HIS A 717 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.043974 restraints weight = 51034.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045553 restraints weight = 26390.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046680 restraints weight = 16914.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047421 restraints weight = 12232.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047987 restraints weight = 9711.098| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2930 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= 0.134 Angle : 0.601 6.767 13988 Z= 0.313 Chirality : 0.042 0.199 1528 Planarity : 0.004 0.056 1789 Dihedral : 8.224 163.501 1386 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.20 % Allowed : 7.21 % Favored : 91.59 % 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: 1.31 (0.24), residues: 1236 helix: 1.21 (0.21), residues: 607 sheet: 1.50 (0.41), residues: 155 loop : 0.37 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 372 TYR 0.011 0.001 TYR A 259 PHE 0.020 0.001 PHE C 255 TRP 0.016 0.002 TRP C 79 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10354) covalent geometry : angle 0.60143 / 0.31 (13982) hydrogen bonds : bond 0.04024 / 2.56 ( 525) hydrogen bonds : angle 4.74630 / 3.39 ( 1446) link_TRANS : bond 0.00145 / 0.07 ( 2) link_TRANS : angle 0.58657 / 0.49 ( 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 100 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8868 (tp30) cc_final: 0.8288 (tp30) REVERT: A 511 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8608 (tt0) REVERT: A 732 LEU cc_start: 0.9765 (mt) cc_final: 0.9364 (tp) REVERT: A 783 MET cc_start: 0.9119 (tmm) cc_final: 0.8912 (tmm) REVERT: C 82 MET cc_start: 0.8435 (tpp) cc_final: 0.8138 (tpp) REVERT: C 313 MET cc_start: 0.9286 (tpt) cc_final: 0.8980 (tpt) REVERT: C 372 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8057 (ttp80) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 0.0845 time to fit residues: 11.9797 Evaluate side-chains 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 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 122 ILE Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 9 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 HIS 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 = 0.058556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044180 restraints weight = 50771.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045782 restraints weight = 26211.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046899 restraints weight = 16764.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047686 restraints weight = 12139.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048180 restraints weight = 9543.639| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10356 Z= 0.120 Angle : 0.572 7.979 13988 Z= 0.295 Chirality : 0.041 0.157 1528 Planarity : 0.004 0.055 1789 Dihedral : 7.864 171.115 1386 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.39 % Allowed : 7.58 % Favored : 91.04 % 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: 1.49 (0.24), residues: 1236 helix: 1.43 (0.21), residues: 606 sheet: 1.50 (0.41), residues: 156 loop : 0.38 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 372 TYR 0.009 0.001 TYR A 175 PHE 0.017 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/Z covalent geometry : bond 0.00264 / 0.12 (10354) covalent geometry : angle 0.57200 / 0.29 (13982) hydrogen bonds : bond 0.03636 / 2.32 ( 525) hydrogen bonds : angle 4.57560 / 3.26 ( 1446) link_TRANS : bond 0.00128 / 0.07 ( 2) link_TRANS : angle 0.47232 / 0.38 ( 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 102 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.258 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: 0.8898 (tp30) cc_final: 0.8338 (tp30) REVERT: A 511 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 732 LEU cc_start: 0.9722 (mt) cc_final: 0.9284 (tp) REVERT: C 176 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7457 (mpp) REVERT: C 313 MET cc_start: 0.9262 (tpt) cc_final: 0.8997 (tpt) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.0679 time to fit residues: 10.1450 Evaluate side-chains 82 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 0.7980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.058254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043906 restraints weight = 50414.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045467 restraints weight = 26133.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046535 restraints weight = 16812.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047317 restraints weight = 12262.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.047798 restraints weight = 9676.208| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3555 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= 0.123 Angle : 0.564 10.072 13988 Z= 0.288 Chirality : 0.041 0.149 1528 Planarity : 0.004 0.053 1789 Dihedral : 7.623 176.570 1386 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.02 % Allowed : 8.87 % Favored : 90.11 % 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: 1.60 (0.24), residues: 1236 helix: 1.59 (0.21), residues: 612 sheet: 1.42 (0.41), residues: 155 loop : 0.36 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 37 TYR 0.010 0.001 TYR A 259 PHE 0.018 0.001 PHE C 255 TRP 0.009 0.001 TRP A 414 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10354) covalent geometry : angle 0.56426 / 0.29 (13982) hydrogen bonds : bond 0.03507 / 2.24 ( 525) hydrogen bonds : angle 4.47512 / 3.18 ( 1446) link_TRANS : bond 0.00098 / 0.05 ( 2) link_TRANS : angle 0.52474 / 0.44 ( 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: 11 poor density : 76 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8885 (tp30) cc_final: 0.8298 (tp30) REVERT: A 511 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8493 (tm-30) REVERT: A 732 LEU cc_start: 0.9711 (mt) cc_final: 0.9278 (tp) REVERT: C 176 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7040 (mpp) outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 0.0816 time to fit residues: 10.4273 Evaluate side-chains 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 78 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.057883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.043499 restraints weight = 51196.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045070 restraints weight = 26499.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046153 restraints weight = 16978.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046791 restraints weight = 12392.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047428 restraints weight = 9999.863| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10356 Z= 0.133 Angle : 0.573 7.954 13988 Z= 0.290 Chirality : 0.040 0.151 1528 Planarity : 0.004 0.052 1789 Dihedral : 7.077 156.221 1386 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.48 % Allowed : 8.69 % Favored : 89.83 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1236 helix: 1.65 (0.21), residues: 616 sheet: 1.33 (0.41), residues: 155 loop : 0.31 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 372 TYR 0.013 0.001 TYR A 127 PHE 0.016 0.001 PHE C 255 TRP 0.008 0.001 TRP A 414 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10354) covalent geometry : angle 0.57291 / 0.29 (13982) hydrogen bonds : bond 0.03482 / 2.22 ( 525) hydrogen bonds : angle 4.42916 / 3.14 ( 1446) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.49664 / 0.41 ( 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 96 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.378 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: 0.8914 (tp30) cc_final: 0.8156 (tp30) REVERT: A 511 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8478 (tm-30) REVERT: C 176 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7323 (mpp) REVERT: C 269 MET cc_start: 0.8333 (mmm) cc_final: 0.7930 (mtt) REVERT: C 299 MET cc_start: 0.8734 (mmm) cc_final: 0.8497 (mmm) REVERT: C 372 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8118 (ttp80) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 0.0840 time to fit residues: 11.7104 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 69 VAL 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 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: 0.7980 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.058406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.044258 restraints weight = 49884.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045816 restraints weight = 25737.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046917 restraints weight = 16402.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.047639 restraints weight = 11893.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048209 restraints weight = 9461.190| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10356 Z= 0.111 Angle : 0.561 7.928 13988 Z= 0.283 Chirality : 0.040 0.149 1528 Planarity : 0.004 0.054 1789 Dihedral : 6.380 127.540 1386 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.39 % Allowed : 9.33 % Favored : 89.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1236 helix: 1.72 (0.21), residues: 616 sheet: 1.23 (0.40), residues: 157 loop : 0.28 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 372 TYR 0.008 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 A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10354) covalent geometry : angle 0.56056 / 0.28 (13982) hydrogen bonds : bond 0.03333 / 2.13 ( 525) hydrogen bonds : angle 4.36342 / 3.11 ( 1446) link_TRANS : bond 0.00120 / 0.06 ( 2) link_TRANS : angle 0.54831 / 0.48 ( 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 98 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 473 GLU cc_start: 0.8886 (tp30) cc_final: 0.8480 (tp30) REVERT: A 511 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 732 LEU cc_start: 0.9619 (mt) cc_final: 0.9199 (tp) REVERT: C 123 MET cc_start: 0.9000 (tpp) cc_final: 0.8761 (mmm) REVERT: C 176 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7248 (mpp) REVERT: C 269 MET cc_start: 0.8280 (mmm) cc_final: 0.8067 (mtm) REVERT: C 305 MET cc_start: 0.9440 (mmm) cc_final: 0.8973 (mmm) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.0809 time to fit residues: 11.5800 Evaluate side-chains 88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN A 645 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044018 restraints weight = 50066.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045572 restraints weight = 25941.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046654 restraints weight = 16602.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047377 restraints weight = 12036.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.047917 restraints weight = 9570.947| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10356 Z= 0.123 Angle : 0.585 8.387 13988 Z= 0.296 Chirality : 0.040 0.170 1528 Planarity : 0.004 0.062 1789 Dihedral : 5.889 102.900 1386 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.29 % Allowed : 10.35 % Favored : 88.35 % 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: 1.60 (0.24), residues: 1236 helix: 1.71 (0.21), residues: 616 sheet: 1.05 (0.39), residues: 160 loop : 0.31 (0.29), residues: 460 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 0.013 0.001 PHE C 255 TRP 0.016 0.002 TRP C 86 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10354) covalent geometry : angle 0.58523 / 0.30 (13982) hydrogen bonds : bond 0.03365 / 2.15 ( 525) hydrogen bonds : angle 4.43983 / 3.15 ( 1446) link_TRANS : bond 0.00110 / 0.06 ( 2) link_TRANS : angle 0.49853 / 0.42 ( 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 96 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.428 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: A 473 GLU cc_start: 0.8884 (tp30) cc_final: 0.8493 (tp30) REVERT: A 511 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 515 MET cc_start: 0.8866 (tpt) cc_final: 0.8641 (tpp) REVERT: C 123 MET cc_start: 0.8996 (tpp) cc_final: 0.8779 (mmm) REVERT: C 269 MET cc_start: 0.8280 (mmm) cc_final: 0.7936 (mtt) REVERT: C 305 MET cc_start: 0.9434 (mmm) cc_final: 0.8942 (mmm) outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.0840 time to fit residues: 11.9060 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 : 0.387 ------------------------------------------------------------------------------- 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 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 122 ILE 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: 0.0670 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.058412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044216 restraints weight = 50347.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045778 restraints weight = 26033.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046871 restraints weight = 16648.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047656 restraints weight = 12104.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048150 restraints weight = 9509.880| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4137 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= 0.116 Angle : 0.598 11.879 13988 Z= 0.297 Chirality : 0.041 0.169 1528 Planarity : 0.004 0.069 1789 Dihedral : 5.515 81.881 1386 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.29 % Allowed : 10.63 % Favored : 88.08 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1236 helix: 1.78 (0.21), residues: 610 sheet: 1.20 (0.39), residues: 157 loop : 0.31 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 372 TYR 0.009 0.001 TYR A 127 PHE 0.013 0.001 PHE C 255 TRP 0.006 0.001 TRP H 1 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10354) covalent geometry : angle 0.59760 / 0.30 (13982) hydrogen bonds : bond 0.03263 / 2.08 ( 525) hydrogen bonds : angle 4.42159 / 3.14 ( 1446) link_TRANS : bond 0.00139 / 0.07 ( 2) link_TRANS : angle 0.45387 / 0.38 ( 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 97 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.404 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: 0.8872 (tp30) cc_final: 0.8515 (tp30) REVERT: A 511 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 269 MET cc_start: 0.8280 (mmm) cc_final: 0.7948 (mtm) REVERT: C 305 MET cc_start: 0.9465 (mmm) cc_final: 0.8987 (mmm) outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.0803 time to fit residues: 11.3264 Evaluate side-chains 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 122 ILE 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: 0.6980 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.058255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044065 restraints weight = 49788.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045615 restraints weight = 25858.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046710 restraints weight = 16584.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047432 restraints weight = 12044.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048001 restraints weight = 9548.642| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10356 Z= 0.126 Angle : 0.643 13.235 13988 Z= 0.317 Chirality : 0.041 0.192 1528 Planarity : 0.004 0.071 1789 Dihedral : 5.353 78.516 1386 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.02 % Allowed : 10.91 % Favored : 88.08 % 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: 1.67 (0.24), residues: 1236 helix: 1.76 (0.22), residues: 609 sheet: 1.19 (0.39), residues: 159 loop : 0.32 (0.29), residues: 468 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 0.014 0.001 PHE C 255 TRP 0.008 0.001 TRP A 374 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10354) covalent geometry : angle 0.64327 / 0.32 (13982) hydrogen bonds : bond 0.03393 / 2.15 ( 525) hydrogen bonds : angle 4.44251 / 3.16 ( 1446) link_TRANS : bond 0.00113 / 0.06 ( 2) link_TRANS : angle 0.45742 / 0.38 ( 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 93 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9307 (mmt180) cc_final: 0.9026 (mmt90) REVERT: A 473 GLU cc_start: 0.8845 (tp30) cc_final: 0.8481 (tp30) REVERT: A 511 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8661 (tm-30) REVERT: C 123 MET cc_start: 0.8980 (tpp) cc_final: 0.8761 (mmm) REVERT: C 269 MET cc_start: 0.8278 (mmm) cc_final: 0.7924 (mtt) REVERT: C 305 MET cc_start: 0.9458 (mmm) cc_final: 0.8978 (mmm) outliers start: 11 outliers final: 11 residues processed: 90 average time/residue: 0.0897 time to fit residues: 11.7482 Evaluate side-chains 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 153 LEU 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 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 HIS 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 = 0.058193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044138 restraints weight = 49977.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045700 restraints weight = 25765.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046774 restraints weight = 16384.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047573 restraints weight = 11902.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048067 restraints weight = 9311.656| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10356 Z= 0.129 Angle : 0.645 12.427 13988 Z= 0.317 Chirality : 0.041 0.183 1528 Planarity : 0.004 0.070 1789 Dihedral : 5.227 78.474 1386 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.02 % Allowed : 11.37 % Favored : 87.62 % 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: 1.70 (0.24), residues: 1236 helix: 1.79 (0.21), residues: 608 sheet: 1.26 (0.40), residues: 160 loop : 0.31 (0.29), residues: 468 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 0.014 0.001 PHE C 255 TRP 0.007 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10354) covalent geometry : angle 0.64468 / 0.32 (13982) hydrogen bonds : bond 0.03381 / 2.15 ( 525) hydrogen bonds : angle 4.43558 / 3.15 ( 1446) link_TRANS : bond 0.00101 / 0.05 ( 2) link_TRANS : angle 0.44653 / 0.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.59 seconds wall clock time: 30 minutes 9.26 seconds (1809.26 seconds total)