Starting phenix.real_space_refine on Fri Feb 14 18:19:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm7_13523/02_2025/7pm7_13523.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm7_13523/02_2025/7pm7_13523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm7_13523/02_2025/7pm7_13523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm7_13523/02_2025/7pm7_13523.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm7_13523/02_2025/7pm7_13523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm7_13523/02_2025/7pm7_13523.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1724 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 7 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: "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: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6070 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 27, 'TRANS': 715} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "A" 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} 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: 6.02, per 1000 atoms: 0.59 Number of scatterers: 10149 At special positions: 0 Unit cell: (107.06, 139.92, 147.34, 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 4 15.00 Mg 2 11.99 O 1894 8.00 N 1724 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 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: 2374 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 15 sheets defined 56.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.284A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.597A 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 66 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.399A 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: 3.578A pdb=" N SER A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.781A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.147A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.895A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.967A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.672A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.597A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.521A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.899A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.592A pdb=" N ILE A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.525A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.508A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.521A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.993A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.042A pdb=" N LYS A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 635 through 653 removed outlier: 4.090A pdb=" N ARG A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.804A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.886A pdb=" N VAL A 720 " --> pdb=" O GLN A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.706A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.690A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.118A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.673A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.535A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.813A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.591A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.518A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.779A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.284A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.566A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.501A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.866A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.408A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.761A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.831A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.608A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 524 hydrogen bonds defined for protein. 1464 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: 3.44 Time building geometry restraints manager: 2.92 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: 1690 1.32 - 1.44: 2740 1.44 - 1.57: 5826 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10364 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.451 0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.74e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.67e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 ... (remaining 10359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13670 2.38 - 4.77: 289 4.77 - 7.15: 30 7.15 - 9.53: 7 9.53 - 11.91: 4 Bond angle restraints: 14000 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 121.70 109.79 11.91 1.80e+00 3.09e-01 4.38e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.80 -4.80 1.10e+00 8.26e-01 1.90e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.28 4.12 1.00e+00 1.00e+00 1.69e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 105.01 6.49 1.70e+00 3.46e-01 1.46e+01 ... (remaining 13995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 6083 32.71 - 65.42: 139 65.42 - 98.12: 28 98.12 - 130.83: 3 130.83 - 163.54: 1 Dihedral angle restraints: 6254 sinusoidal: 2572 harmonic: 3682 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 300.00 136.46 163.54 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 66.38 -126.38 1 2.00e+01 2.50e-03 3.82e+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 300.00 176.15 123.85 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1011 0.041 - 0.083: 353 0.083 - 0.124: 130 0.124 - 0.165: 27 0.165 - 0.207: 9 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 364 " pdb=" N MET A 364 " pdb=" C MET A 364 " pdb=" CB MET A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE C 124 " pdb=" N PHE C 124 " pdb=" C PHE C 124 " pdb=" CB PHE C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1527 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.114 9.50e-02 1.11e+02 6.65e-02 2.44e+01 pdb=" NE ARG A 248 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.284 9.50e-02 1.11e+02 1.31e-01 2.06e+01 pdb=" NE ARG A 213 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " -0.101 9.50e-02 1.11e+02 5.85e-02 1.85e+01 pdb=" NE ARG C 312 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.020 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 16 2.37 - 3.00: 5470 3.00 - 3.63: 15098 3.63 - 4.27: 22662 4.27 - 4.90: 38361 Nonbonded interactions: 81607 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.140 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.141 3.040 nonbonded pdb=" O PHE A 698 " pdb=" NH1 ARG A 701 " model vdw 2.154 3.120 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.220 2.170 ... (remaining 81602 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.004 0.121 10364 Z= 0.272 Angle : 0.851 11.913 14000 Z= 0.500 Chirality : 0.050 0.207 1530 Planarity : 0.008 0.131 1785 Dihedral : 15.671 163.540 3874 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.09 % Allowed : 0.46 % Favored : 99.44 % 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: -1.31 (0.21), residues: 1231 helix: -1.57 (0.17), residues: 589 sheet: 0.64 (0.39), residues: 148 loop : -0.16 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP C 340 HIS 0.007 0.001 HIS C 371 PHE 0.032 0.002 PHE C 255 TYR 0.044 0.006 TYR A 113 ARG 0.083 0.011 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 LEU cc_start: 0.8896 (mt) cc_final: 0.8164 (mp) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.2516 time to fit residues: 52.8669 Evaluate side-chains 92 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 191 ASN A 264 GLN A 354 HIS A 395 HIS A 462 GLN A 463 GLN C 12 ASN C 162 ASN C 173 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.075658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.054908 restraints weight = 35348.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057023 restraints weight = 16543.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058419 restraints weight = 10146.691| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10364 Z= 0.202 Angle : 0.636 7.840 14000 Z= 0.332 Chirality : 0.044 0.282 1530 Planarity : 0.004 0.042 1785 Dihedral : 9.465 142.587 1404 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.74 % Allowed : 6.01 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.24), residues: 1231 helix: 0.77 (0.20), residues: 616 sheet: 0.94 (0.38), residues: 160 loop : 0.60 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.008 0.001 HIS C 275 PHE 0.024 0.002 PHE C 255 TYR 0.032 0.001 TYR A 102 ARG 0.006 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8803 (mmm) cc_final: 0.8370 (tpp) REVERT: A 478 MET cc_start: 0.8321 (mmp) cc_final: 0.7818 (mmp) REVERT: A 484 TRP cc_start: 0.6634 (m-10) cc_final: 0.6197 (m-10) REVERT: A 500 GLU cc_start: 0.8828 (tt0) cc_final: 0.8387 (tt0) REVERT: C 179 ASP cc_start: 0.7908 (p0) cc_final: 0.7629 (p0) outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 0.1934 time to fit residues: 31.6934 Evaluate side-chains 86 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN C 12 ASN C 59 GLN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.075399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054660 restraints weight = 36796.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056791 restraints weight = 16970.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058217 restraints weight = 10328.984| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10364 Z= 0.171 Angle : 0.564 7.621 14000 Z= 0.289 Chirality : 0.042 0.177 1530 Planarity : 0.004 0.050 1785 Dihedral : 7.571 93.516 1403 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.48 % Allowed : 6.85 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1231 helix: 1.44 (0.21), residues: 615 sheet: 1.22 (0.40), residues: 159 loop : 0.77 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.016 0.001 PHE C 255 TYR 0.021 0.001 TYR A 102 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9487 (mp) cc_final: 0.9247 (mm) REVERT: A 135 MET cc_start: 0.8837 (mmm) cc_final: 0.8585 (tpp) REVERT: A 172 SER cc_start: 0.9154 (m) cc_final: 0.8952 (p) REVERT: A 478 MET cc_start: 0.8244 (mmp) cc_final: 0.7901 (mmp) REVERT: A 484 TRP cc_start: 0.6525 (m-10) cc_final: 0.6151 (m-10) REVERT: A 500 GLU cc_start: 0.8783 (tt0) cc_final: 0.8295 (tt0) REVERT: A 775 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: C 111 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.7991 (p0) REVERT: C 137 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8111 (mm-40) REVERT: C 225 ASN cc_start: 0.8683 (m110) cc_final: 0.8478 (t0) outliers start: 16 outliers final: 7 residues processed: 98 average time/residue: 0.2344 time to fit residues: 33.3631 Evaluate side-chains 86 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.6980 chunk 122 optimal weight: 0.1980 chunk 118 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054657 restraints weight = 36588.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056759 restraints weight = 16886.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058170 restraints weight = 10253.553| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10364 Z= 0.163 Angle : 0.559 7.311 14000 Z= 0.282 Chirality : 0.041 0.174 1530 Planarity : 0.004 0.052 1785 Dihedral : 6.985 84.811 1403 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.20 % Allowed : 8.23 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.24), residues: 1231 helix: 1.73 (0.21), residues: 604 sheet: 1.35 (0.40), residues: 159 loop : 0.81 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS C 275 PHE 0.016 0.001 PHE A 360 TYR 0.017 0.001 TYR A 102 ARG 0.009 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4445 (mmt) cc_final: 0.4075 (mmt) REVERT: A 40 LEU cc_start: 0.9539 (mp) cc_final: 0.9299 (mm) REVERT: A 135 MET cc_start: 0.8826 (mmm) cc_final: 0.8287 (tpp) REVERT: A 172 SER cc_start: 0.9146 (m) cc_final: 0.8939 (p) REVERT: A 478 MET cc_start: 0.8187 (mmp) cc_final: 0.7896 (mmp) REVERT: A 484 TRP cc_start: 0.6558 (m-10) cc_final: 0.6277 (m-10) REVERT: A 500 GLU cc_start: 0.8805 (tt0) cc_final: 0.8286 (tt0) REVERT: A 515 MET cc_start: 0.8877 (tpt) cc_final: 0.8413 (tpt) REVERT: C 162 ASN cc_start: 0.8493 (m-40) cc_final: 0.8276 (m-40) REVERT: C 225 ASN cc_start: 0.8712 (m110) cc_final: 0.8461 (t0) REVERT: C 242 LEU cc_start: 0.8552 (mp) cc_final: 0.8339 (mp) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 0.2500 time to fit residues: 34.7442 Evaluate side-chains 83 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.074131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053441 restraints weight = 36750.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.055535 restraints weight = 17074.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056920 restraints weight = 10435.024| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10364 Z= 0.195 Angle : 0.555 7.080 14000 Z= 0.280 Chirality : 0.041 0.174 1530 Planarity : 0.004 0.053 1785 Dihedral : 6.546 67.741 1403 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.20 % Allowed : 8.70 % Favored : 90.10 % 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: 2.04 (0.24), residues: 1231 helix: 1.87 (0.21), residues: 603 sheet: 1.41 (0.40), residues: 159 loop : 0.81 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS C 275 PHE 0.015 0.001 PHE A 360 TYR 0.015 0.001 TYR A 102 ARG 0.010 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 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: B 120 MET cc_start: 0.4536 (mmt) cc_final: 0.4117 (mmt) REVERT: A 40 LEU cc_start: 0.9539 (mp) cc_final: 0.9262 (mm) REVERT: A 478 MET cc_start: 0.8238 (mmp) cc_final: 0.7942 (mmp) REVERT: A 484 TRP cc_start: 0.6621 (m-10) cc_final: 0.6397 (m-10) REVERT: A 500 GLU cc_start: 0.8849 (tt0) cc_final: 0.8351 (tt0) REVERT: C 225 ASN cc_start: 0.8723 (m110) cc_final: 0.8487 (t0) REVERT: C 305 MET cc_start: 0.9115 (mmm) cc_final: 0.8894 (mmt) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.2327 time to fit residues: 31.0328 Evaluate side-chains 81 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.073133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.052657 restraints weight = 36771.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054717 restraints weight = 17031.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056097 restraints weight = 10395.335| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10364 Z= 0.227 Angle : 0.577 7.717 14000 Z= 0.291 Chirality : 0.042 0.176 1530 Planarity : 0.004 0.055 1785 Dihedral : 6.434 67.168 1403 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.39 % Allowed : 8.79 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.25), residues: 1231 helix: 1.77 (0.21), residues: 614 sheet: 1.28 (0.41), residues: 155 loop : 0.69 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS A 354 PHE 0.015 0.001 PHE C 255 TYR 0.015 0.001 TYR A 102 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.5976 (tmm) cc_final: 0.5084 (tmm) REVERT: B 120 MET cc_start: 0.4660 (mmt) cc_final: 0.4190 (mmt) REVERT: A 40 LEU cc_start: 0.9556 (mp) cc_final: 0.9275 (mm) REVERT: A 478 MET cc_start: 0.8228 (mmp) cc_final: 0.7789 (mmm) REVERT: A 484 TRP cc_start: 0.6725 (m-10) cc_final: 0.6296 (m-10) REVERT: A 500 GLU cc_start: 0.8865 (tt0) cc_final: 0.8341 (tt0) REVERT: A 515 MET cc_start: 0.8880 (tpt) cc_final: 0.8510 (tpt) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 0.2401 time to fit residues: 29.7500 Evaluate side-chains 77 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.053901 restraints weight = 36808.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.055998 restraints weight = 16919.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057380 restraints weight = 10250.437| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10364 Z= 0.153 Angle : 0.555 7.816 14000 Z= 0.275 Chirality : 0.041 0.174 1530 Planarity : 0.004 0.057 1785 Dihedral : 6.104 67.562 1403 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 9.16 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1231 helix: 1.94 (0.21), residues: 609 sheet: 1.35 (0.42), residues: 155 loop : 0.77 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.011 0.001 HIS A 418 PHE 0.015 0.001 PHE A 360 TYR 0.016 0.001 TYR A 102 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4511 (mmt) cc_final: 0.4269 (mmt) REVERT: A 40 LEU cc_start: 0.9534 (mp) cc_final: 0.9261 (mm) REVERT: A 354 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.8620 (t70) REVERT: A 478 MET cc_start: 0.8148 (mmp) cc_final: 0.7710 (mmm) REVERT: A 484 TRP cc_start: 0.6723 (m-10) cc_final: 0.6252 (m-10) REVERT: A 500 GLU cc_start: 0.8851 (tt0) cc_final: 0.8318 (tt0) REVERT: A 515 MET cc_start: 0.8834 (tpt) cc_final: 0.8353 (tpt) REVERT: C 154 ASP cc_start: 0.8374 (t70) cc_final: 0.7568 (t70) REVERT: C 162 ASN cc_start: 0.8444 (m-40) cc_final: 0.8213 (m-40) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.2157 time to fit residues: 27.1800 Evaluate side-chains 84 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.073396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.052865 restraints weight = 36742.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.054954 restraints weight = 17035.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056350 restraints weight = 10368.616| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10364 Z= 0.209 Angle : 0.574 9.260 14000 Z= 0.285 Chirality : 0.041 0.173 1530 Planarity : 0.004 0.055 1785 Dihedral : 6.053 67.316 1403 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.20 % Allowed : 10.08 % Favored : 88.71 % 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: 2.08 (0.25), residues: 1231 helix: 1.91 (0.21), residues: 608 sheet: 1.34 (0.40), residues: 165 loop : 0.81 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.011 0.001 HIS A 418 PHE 0.014 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.7561 (mmm) cc_final: 0.6596 (mmm) REVERT: B 120 MET cc_start: 0.4820 (mmt) cc_final: 0.4341 (mmt) REVERT: A 40 LEU cc_start: 0.9507 (mp) cc_final: 0.9232 (mm) REVERT: A 354 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8624 (t70) REVERT: A 500 GLU cc_start: 0.8841 (tt0) cc_final: 0.8321 (tt0) REVERT: A 515 MET cc_start: 0.8776 (tpt) cc_final: 0.8347 (tpt) REVERT: C 154 ASP cc_start: 0.8375 (t70) cc_final: 0.7600 (t70) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.2227 time to fit residues: 28.0733 Evaluate side-chains 80 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 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 = 0.3468 r_free = 0.3468 target = 0.073483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.052968 restraints weight = 36501.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055032 restraints weight = 16905.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056413 restraints weight = 10279.276| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10364 Z= 0.198 Angle : 0.586 9.640 14000 Z= 0.290 Chirality : 0.041 0.173 1530 Planarity : 0.004 0.056 1785 Dihedral : 5.942 67.249 1403 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.20 % Allowed : 10.27 % Favored : 88.53 % 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: 2.04 (0.25), residues: 1231 helix: 1.87 (0.22), residues: 608 sheet: 1.32 (0.41), residues: 165 loop : 0.81 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 484 HIS 0.011 0.001 HIS A 418 PHE 0.015 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.003 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.128 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: 0.7678 (mmm) cc_final: 0.6762 (mmm) REVERT: B 120 MET cc_start: 0.4749 (mmt) cc_final: 0.4395 (mmt) REVERT: A 40 LEU cc_start: 0.9510 (mp) cc_final: 0.9235 (mm) REVERT: A 354 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8579 (t70) REVERT: A 478 MET cc_start: 0.8654 (mmp) cc_final: 0.8235 (mmp) REVERT: A 484 TRP cc_start: 0.6840 (m-10) cc_final: 0.6538 (m100) REVERT: A 500 GLU cc_start: 0.8853 (tt0) cc_final: 0.8334 (tt0) REVERT: A 515 MET cc_start: 0.8731 (tpt) cc_final: 0.8327 (tpt) REVERT: C 154 ASP cc_start: 0.8366 (t70) cc_final: 0.7553 (t70) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.2295 time to fit residues: 27.9800 Evaluate side-chains 80 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.073771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053191 restraints weight = 36748.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055266 restraints weight = 16999.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.056650 restraints weight = 10359.098| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10364 Z= 0.190 Angle : 0.591 10.540 14000 Z= 0.293 Chirality : 0.041 0.172 1530 Planarity : 0.004 0.058 1785 Dihedral : 5.821 67.492 1403 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.93 % Allowed : 10.55 % Favored : 88.53 % 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: 2.07 (0.25), residues: 1231 helix: 1.90 (0.22), residues: 608 sheet: 1.33 (0.41), residues: 164 loop : 0.82 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 484 HIS 0.010 0.001 HIS A 418 PHE 0.015 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.004 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 2.129 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 40 LEU cc_start: 0.9531 (mp) cc_final: 0.9260 (mm) REVERT: A 354 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8574 (t70) REVERT: A 478 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (mmp) REVERT: A 500 GLU cc_start: 0.8863 (tt0) cc_final: 0.8628 (tt0) REVERT: A 515 MET cc_start: 0.8721 (tpt) cc_final: 0.8321 (tpt) REVERT: C 154 ASP cc_start: 0.8365 (t70) cc_final: 0.7424 (t70) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.2288 time to fit residues: 27.5358 Evaluate side-chains 82 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.073964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053491 restraints weight = 36310.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.055557 restraints weight = 16807.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056929 restraints weight = 10248.551| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10364 Z= 0.180 Angle : 0.599 11.045 14000 Z= 0.297 Chirality : 0.041 0.215 1530 Planarity : 0.004 0.058 1785 Dihedral : 5.730 67.749 1403 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.93 % Allowed : 10.45 % Favored : 88.62 % 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: 2.07 (0.25), residues: 1231 helix: 1.91 (0.22), residues: 608 sheet: 1.36 (0.40), residues: 164 loop : 0.80 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 484 HIS 0.010 0.001 HIS A 418 PHE 0.016 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.003 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.69 seconds wall clock time: 61 minutes 4.81 seconds (3664.81 seconds total)