Starting phenix.real_space_refine on Mon Jul 28 15:41:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plx_13505/07_2025/7plx_13505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plx_13505/07_2025/7plx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2025/7plx_13505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2025/7plx_13505.map" model { file = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2025/7plx_13505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plx_13505/07_2025/7plx_13505.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1722 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.80, per 1000 atoms: 0.67 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 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: 1.39 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: 3.61 Time building geometry restraints manager: 3.40 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: 2.120 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (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 TRP 0.036 0.004 TRP C 79 HIS 0.010 0.002 HIS A 81 PHE 0.032 0.002 PHE A 564 TYR 0.038 0.006 TYR C 306 ARG 0.075 0.012 ARG A 278 Details of bonding type rmsd link_TRANS : bond 0.00653 ( 2) link_TRANS : angle 4.73778 ( 6) hydrogen bonds : bond 0.15905 ( 525) hydrogen bonds : angle 6.83003 ( 1446) covalent geometry : bond 0.00463 (10354) covalent geometry : angle 0.82317 (13982) *********************** 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 : 1.190 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: 0.2810 time to fit residues: 60.4623 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 : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 497 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A 657 HIS A 717 GLN A 755 GLN A 775 GLN C 111 ASN C 128 ASN C 162 ASN C 280 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.044113 restraints weight = 50923.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045663 restraints weight = 26356.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046787 restraints weight = 17012.266| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10356 Z= 0.164 Angle : 0.670 7.530 13988 Z= 0.356 Chirality : 0.043 0.158 1528 Planarity : 0.005 0.054 1789 Dihedral : 9.147 157.103 1396 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.29 % Allowed : 5.64 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1236 helix: 0.66 (0.20), residues: 609 sheet: 1.18 (0.39), residues: 159 loop : 0.33 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 79 HIS 0.010 0.002 HIS C 275 PHE 0.024 0.002 PHE C 255 TYR 0.019 0.002 TYR C 279 ARG 0.007 0.001 ARG A 178 Details of bonding type rmsd link_TRANS : bond 0.00269 ( 2) link_TRANS : angle 1.29849 ( 6) hydrogen bonds : bond 0.04680 ( 525) hydrogen bonds : angle 4.99385 ( 1446) covalent geometry : bond 0.00359 (10354) covalent geometry : angle 0.66955 (13982) *********************** 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 110 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8257 (m-80) cc_final: 0.8054 (m-80) REVERT: A 473 GLU cc_start: 0.8817 (tp30) cc_final: 0.8104 (tp30) REVERT: A 511 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 761 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9124 (tptt) REVERT: A 783 MET cc_start: 0.9281 (tmm) cc_final: 0.9071 (tmm) outliers start: 14 outliers final: 7 residues processed: 105 average time/residue: 0.2094 time to fit residues: 32.8097 Evaluate side-chains 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 99 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 117 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 645 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.058925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.044507 restraints weight = 50901.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046132 restraints weight = 26166.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047271 restraints weight = 16650.641| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2976 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 : 0.596 7.562 13988 Z= 0.307 Chirality : 0.042 0.198 1528 Planarity : 0.004 0.056 1789 Dihedral : 8.637 165.247 1396 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1236 helix: 1.23 (0.21), residues: 609 sheet: 1.60 (0.41), residues: 151 loop : 0.33 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 414 HIS 0.007 0.001 HIS C 275 PHE 0.020 0.001 PHE C 255 TYR 0.011 0.001 TYR A 127 ARG 0.010 0.001 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00253 ( 2) link_TRANS : angle 1.12567 ( 6) hydrogen bonds : bond 0.03891 ( 525) hydrogen bonds : angle 4.66501 ( 1446) covalent geometry : bond 0.00263 (10354) covalent geometry : angle 0.59534 (13982) *********************** 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 102 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8313 (m-80) cc_final: 0.8052 (m-80) REVERT: A 473 GLU cc_start: 0.8892 (tp30) cc_final: 0.8341 (tp30) REVERT: A 511 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 732 LEU cc_start: 0.9791 (mt) cc_final: 0.9254 (tp) REVERT: A 783 MET cc_start: 0.9180 (tmm) cc_final: 0.8894 (tmm) REVERT: C 372 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8081 (ttp80) outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 0.2072 time to fit residues: 30.3350 Evaluate side-chains 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 14 optimal weight: 0.0270 chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- 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** A 645 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.059269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044884 restraints weight = 50212.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046497 restraints weight = 26012.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047632 restraints weight = 16641.004| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3364 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= 0.105 Angle : 0.551 6.650 13988 Z= 0.284 Chirality : 0.040 0.181 1528 Planarity : 0.004 0.056 1789 Dihedral : 8.247 174.374 1396 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.39 % Allowed : 7.67 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1236 helix: 1.51 (0.21), residues: 605 sheet: 1.49 (0.41), residues: 156 loop : 0.42 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 PHE 0.020 0.001 PHE C 255 TYR 0.010 0.001 TYR A 711 ARG 0.006 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00152 ( 2) link_TRANS : angle 0.83227 ( 6) hydrogen bonds : bond 0.03475 ( 525) hydrogen bonds : angle 4.46385 ( 1446) covalent geometry : bond 0.00226 (10354) covalent geometry : angle 0.55090 (13982) *********************** 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 105 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.156 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: 0.8936 (tp30) cc_final: 0.8376 (tp30) REVERT: A 511 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8524 (tm-30) REVERT: A 732 LEU cc_start: 0.9754 (mt) cc_final: 0.9197 (tp) REVERT: C 176 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7530 (mpp) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 0.1840 time to fit residues: 27.7380 Evaluate side-chains 82 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 357 LEU 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 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 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3353 r_free = 0.3353 target = 0.058707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044288 restraints weight = 50520.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045834 restraints weight = 26239.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046969 restraints weight = 16889.994| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3572 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= 0.121 Angle : 0.561 8.544 13988 Z= 0.285 Chirality : 0.040 0.172 1528 Planarity : 0.004 0.055 1789 Dihedral : 7.928 172.222 1396 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.29 % Allowed : 8.87 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1236 helix: 1.61 (0.21), residues: 615 sheet: 1.42 (0.41), residues: 155 loop : 0.34 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 414 HIS 0.005 0.001 HIS A 418 PHE 0.015 0.001 PHE C 255 TYR 0.012 0.001 TYR A 79 ARG 0.005 0.000 ARG B 37 Details of bonding type rmsd link_TRANS : bond 0.00071 ( 2) link_TRANS : angle 0.82283 ( 6) hydrogen bonds : bond 0.03449 ( 525) hydrogen bonds : angle 4.40521 ( 1446) covalent geometry : bond 0.00270 (10354) covalent geometry : angle 0.56072 (13982) *********************** 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 94 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.992 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: 0.8903 (tp30) cc_final: 0.8328 (tp30) REVERT: A 511 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 732 LEU cc_start: 0.9744 (mt) cc_final: 0.9197 (tp) REVERT: C 176 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7179 (mpp) REVERT: C 269 MET cc_start: 0.8356 (mmm) cc_final: 0.8150 (mtp) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.2479 time to fit residues: 32.4539 Evaluate side-chains 86 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.058913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044514 restraints weight = 50533.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046066 restraints weight = 26175.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047179 restraints weight = 16871.762| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3741 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= 0.107 Angle : 0.560 7.634 13988 Z= 0.282 Chirality : 0.040 0.165 1528 Planarity : 0.004 0.053 1789 Dihedral : 7.408 153.382 1396 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.39 % Allowed : 9.43 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1236 helix: 1.73 (0.21), residues: 617 sheet: 1.39 (0.41), residues: 155 loop : 0.31 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.015 0.001 PHE C 255 TYR 0.012 0.001 TYR A 127 ARG 0.008 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00129 ( 2) link_TRANS : angle 0.82997 ( 6) hydrogen bonds : bond 0.03296 ( 525) hydrogen bonds : angle 4.33630 ( 1446) covalent geometry : bond 0.00237 (10354) covalent geometry : angle 0.55966 (13982) *********************** 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: 15 poor density : 81 time to evaluate : 1.322 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: 0.8786 (tp30) cc_final: 0.8287 (tp30) REVERT: A 511 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8523 (tm-30) REVERT: C 176 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7373 (mpp) REVERT: C 269 MET cc_start: 0.8345 (mmm) cc_final: 0.8120 (mtp) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.2889 time to fit residues: 38.4305 Evaluate side-chains 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 265 LEU 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 54 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.058314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.043921 restraints weight = 50910.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.045493 restraints weight = 26396.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046577 restraints weight = 16920.185| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3876 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= 0.127 Angle : 0.569 7.713 13988 Z= 0.286 Chirality : 0.040 0.161 1528 Planarity : 0.004 0.052 1789 Dihedral : 6.648 116.695 1396 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.66 % Allowed : 9.70 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1236 helix: 1.71 (0.21), residues: 622 sheet: 1.30 (0.41), residues: 156 loop : 0.28 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.015 0.001 PHE C 255 TYR 0.011 0.001 TYR A 259 ARG 0.009 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00057 ( 2) link_TRANS : angle 0.80868 ( 6) hydrogen bonds : bond 0.03357 ( 525) hydrogen bonds : angle 4.35296 ( 1446) covalent geometry : bond 0.00284 (10354) covalent geometry : angle 0.56859 (13982) *********************** 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 99 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9066 (ttm) cc_final: 0.8799 (tpp) REVERT: A 323 MET cc_start: 0.8897 (mmm) cc_final: 0.8480 (tmm) REVERT: A 473 GLU cc_start: 0.8815 (tp30) cc_final: 0.8299 (tp30) REVERT: A 511 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 732 LEU cc_start: 0.9722 (mt) cc_final: 0.9221 (tp) REVERT: C 123 MET cc_start: 0.9015 (tpp) cc_final: 0.8777 (mmm) REVERT: C 176 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: C 269 MET cc_start: 0.8350 (mmm) cc_final: 0.7964 (mtt) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.2413 time to fit residues: 33.6472 Evaluate side-chains 91 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 265 LEU 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 69 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.058791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.044367 restraints weight = 50608.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045943 restraints weight = 26058.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047087 restraints weight = 16710.047| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4000 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= 0.107 Angle : 0.577 10.825 13988 Z= 0.288 Chirality : 0.040 0.165 1528 Planarity : 0.004 0.055 1789 Dihedral : 6.262 96.957 1396 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.29 % Allowed : 10.07 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1236 helix: 1.82 (0.21), residues: 616 sheet: 1.22 (0.40), residues: 157 loop : 0.28 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.013 0.001 PHE C 255 TYR 0.011 0.001 TYR A 127 ARG 0.008 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00134 ( 2) link_TRANS : angle 0.82122 ( 6) hydrogen bonds : bond 0.03244 ( 525) hydrogen bonds : angle 4.34113 ( 1446) covalent geometry : bond 0.00240 (10354) covalent geometry : angle 0.57735 (13982) *********************** 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 100 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.058 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: 0.9106 (ttm) cc_final: 0.8857 (mmt) REVERT: A 370 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8522 (mm-30) REVERT: A 473 GLU cc_start: 0.8929 (tp30) cc_final: 0.8410 (tp30) REVERT: A 511 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 732 LEU cc_start: 0.9718 (mt) cc_final: 0.9206 (tp) REVERT: C 47 MET cc_start: 0.7874 (ppp) cc_final: 0.7542 (ppp) REVERT: C 176 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: C 269 MET cc_start: 0.8375 (mmm) cc_final: 0.8127 (mtm) REVERT: C 305 MET cc_start: 0.9436 (mmm) cc_final: 0.8941 (mmm) outliers start: 14 outliers final: 12 residues processed: 93 average time/residue: 0.2538 time to fit residues: 36.2783 Evaluate side-chains 94 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET 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 265 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.058513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.044260 restraints weight = 50193.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045832 restraints weight = 25897.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046928 restraints weight = 16536.620| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4095 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= 0.121 Angle : 0.604 9.492 13988 Z= 0.300 Chirality : 0.041 0.188 1528 Planarity : 0.004 0.052 1789 Dihedral : 6.007 82.367 1396 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.20 % Allowed : 11.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1236 helix: 1.76 (0.21), residues: 622 sheet: 1.16 (0.39), residues: 157 loop : 0.30 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.013 0.001 PHE C 255 TYR 0.011 0.001 TYR A 127 ARG 0.007 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00077 ( 2) link_TRANS : angle 0.80613 ( 6) hydrogen bonds : bond 0.03271 ( 525) hydrogen bonds : angle 4.32431 ( 1446) covalent geometry : bond 0.00271 (10354) covalent geometry : angle 0.60347 (13982) *********************** 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 96 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8896 (tp30) cc_final: 0.8352 (tp30) REVERT: A 511 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 515 MET cc_start: 0.8827 (tpt) cc_final: 0.8591 (tpp) REVERT: A 732 LEU cc_start: 0.9710 (mt) cc_final: 0.9192 (tp) REVERT: C 47 MET cc_start: 0.7765 (ppp) cc_final: 0.7485 (ppp) REVERT: C 123 MET cc_start: 0.8987 (tpp) cc_final: 0.8773 (mmm) REVERT: C 269 MET cc_start: 0.8344 (mmm) cc_final: 0.7999 (mtt) REVERT: C 305 MET cc_start: 0.9428 (mmm) cc_final: 0.8914 (mmm) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.2021 time to fit residues: 26.9942 Evaluate side-chains 86 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 265 LEU 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 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.057541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043672 restraints weight = 50868.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045209 restraints weight = 26266.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046256 restraints weight = 16788.369| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.156 Angle : 0.642 10.916 13988 Z= 0.321 Chirality : 0.042 0.171 1528 Planarity : 0.004 0.054 1789 Dihedral : 5.943 81.616 1396 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 11.18 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1236 helix: 1.74 (0.21), residues: 609 sheet: 1.13 (0.39), residues: 159 loop : 0.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.014 0.001 PHE C 255 TYR 0.013 0.001 TYR A 259 ARG 0.006 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00042 ( 2) link_TRANS : angle 0.78284 ( 6) hydrogen bonds : bond 0.03535 ( 525) hydrogen bonds : angle 4.42993 ( 1446) covalent geometry : bond 0.00348 (10354) covalent geometry : angle 0.64231 (13982) ********************** 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 89 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8891 (tp30) cc_final: 0.8303 (tp30) REVERT: A 515 MET cc_start: 0.8870 (tpt) cc_final: 0.8656 (tpp) REVERT: A 732 LEU cc_start: 0.9714 (mt) cc_final: 0.9228 (tp) REVERT: C 47 MET cc_start: 0.7685 (ppp) cc_final: 0.7432 (ppp) REVERT: C 269 MET cc_start: 0.8297 (mmm) cc_final: 0.7901 (mtt) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.2044 time to fit residues: 25.5843 Evaluate side-chains 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** C 78 ASN ** 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 = 0.3359 r_free = 0.3359 target = 0.058534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044470 restraints weight = 50073.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046028 restraints weight = 25551.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047119 restraints weight = 16163.969| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10356 Z= 0.116 Angle : 0.642 12.510 13988 Z= 0.318 Chirality : 0.042 0.169 1528 Planarity : 0.004 0.053 1789 Dihedral : 5.756 81.540 1396 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.92 % Allowed : 11.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1236 helix: 1.82 (0.22), residues: 608 sheet: 1.11 (0.39), residues: 159 loop : 0.32 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.003 0.001 HIS A 418 PHE 0.013 0.001 PHE C 255 TYR 0.009 0.001 TYR A 119 ARG 0.006 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00130 ( 2) link_TRANS : angle 0.80201 ( 6) hydrogen bonds : bond 0.03403 ( 525) hydrogen bonds : angle 4.36833 ( 1446) covalent geometry : bond 0.00261 (10354) covalent geometry : angle 0.64215 (13982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.18 seconds wall clock time: 65 minutes 57.06 seconds (3957.06 seconds total)