Starting phenix.real_space_refine on Mon Jul 28 16:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm7_13523/07_2025/7pm7_13523.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm7_13523/07_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_13523/07_2025/7pm7_13523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm7_13523/07_2025/7pm7_13523.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm7_13523/07_2025/7pm7_13523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm7_13523/07_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-5711/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: 7.47, per 1000 atoms: 0.74 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: 2.48 Conformation dependent library (CDL) restraints added in 1.6 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: 3.03 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: 5.40 Time building geometry restraints manager: 3.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 372.480 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.130 Set scattering table: 0.230 Process input model: 39.640 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 419.290 ------------------------------------------------------------------------------- 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 10366 Z= 0.215 Angle : 0.856 11.913 14006 Z= 0.502 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 Details of bonding type rmsd link_TRANS : bond 0.00928 ( 2) link_TRANS : angle 4.24947 ( 6) hydrogen bonds : bond 0.17411 ( 522) hydrogen bonds : angle 7.48472 ( 1464) covalent geometry : bond 0.00441 (10364) covalent geometry : angle 0.85117 (14000) *********************** 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 : 1.653 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: 0.3463 time to fit residues: 74.5994 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 : 1.212 ------------------------------------------------------------------------------- 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 = 0.054909 restraints weight = 35348.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057014 restraints weight = 16543.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058398 restraints weight = 10154.165| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 10366 Z= 0.144 Angle : 0.636 7.840 14006 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 Details of bonding type rmsd link_TRANS : bond 0.00154 ( 2) link_TRANS : angle 1.37380 ( 6) hydrogen bonds : bond 0.04144 ( 522) hydrogen bonds : angle 5.02759 ( 1464) covalent geometry : bond 0.00316 (10364) covalent geometry : angle 0.63571 (14000) *********************** 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 : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8795 (mmm) cc_final: 0.8365 (tpp) REVERT: A 478 MET cc_start: 0.8323 (mmp) cc_final: 0.7819 (mmp) REVERT: A 484 TRP cc_start: 0.6631 (m-10) cc_final: 0.6194 (m-10) REVERT: A 500 GLU cc_start: 0.8828 (tt0) cc_final: 0.8387 (tt0) REVERT: C 179 ASP cc_start: 0.7912 (p0) cc_final: 0.7629 (p0) outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 0.2141 time to fit residues: 35.9437 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 : 2.301 ------------------------------------------------------------------------------- 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: 1.9990 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.053960 restraints weight = 36521.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056054 restraints weight = 16821.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057457 restraints weight = 10229.976| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10366 Z= 0.138 Angle : 0.573 7.477 14006 Z= 0.294 Chirality : 0.042 0.179 1530 Planarity : 0.004 0.050 1785 Dihedral : 7.627 94.331 1403 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.39 % Allowed : 7.49 % Favored : 91.12 % 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: 1.64 (0.24), residues: 1231 helix: 1.44 (0.21), residues: 613 sheet: 1.21 (0.40), residues: 159 loop : 0.77 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.017 0.001 PHE C 255 TYR 0.022 0.001 TYR A 102 ARG 0.006 0.000 ARG B 110 Details of bonding type rmsd link_TRANS : bond 0.00182 ( 2) link_TRANS : angle 0.88720 ( 6) hydrogen bonds : bond 0.03749 ( 522) hydrogen bonds : angle 4.58039 ( 1464) covalent geometry : bond 0.00310 (10364) covalent geometry : angle 0.57233 (14000) *********************** 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 100 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4603 (mtt) cc_final: 0.3535 (mmt) REVERT: A 135 MET cc_start: 0.8862 (mmm) cc_final: 0.8616 (tpp) REVERT: A 172 SER cc_start: 0.9148 (m) cc_final: 0.8940 (p) REVERT: A 478 MET cc_start: 0.8299 (mmp) cc_final: 0.7908 (mmp) REVERT: A 484 TRP cc_start: 0.6598 (m-10) cc_final: 0.6235 (m-10) REVERT: A 500 GLU cc_start: 0.8812 (tt0) cc_final: 0.8315 (tt0) REVERT: A 775 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: C 137 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8167 (mm-40) REVERT: C 225 ASN cc_start: 0.8702 (m110) cc_final: 0.8496 (t0) outliers start: 15 outliers final: 7 residues processed: 95 average time/residue: 0.2472 time to fit residues: 34.3877 Evaluate side-chains 81 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 122 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.073852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053349 restraints weight = 36719.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055429 restraints weight = 17024.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056817 restraints weight = 10442.772| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10366 Z= 0.141 Angle : 0.567 7.206 14006 Z= 0.287 Chirality : 0.042 0.176 1530 Planarity : 0.004 0.054 1785 Dihedral : 7.236 93.064 1403 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.11 % Allowed : 8.05 % Favored : 90.84 % 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: 1.80 (0.24), residues: 1231 helix: 1.64 (0.21), residues: 609 sheet: 1.23 (0.39), residues: 165 loop : 0.76 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.016 0.001 PHE A 360 TYR 0.016 0.001 TYR A 102 ARG 0.005 0.000 ARG B 110 Details of bonding type rmsd link_TRANS : bond 0.00209 ( 2) link_TRANS : angle 0.88064 ( 6) hydrogen bonds : bond 0.03615 ( 522) hydrogen bonds : angle 4.57104 ( 1464) covalent geometry : bond 0.00320 (10364) covalent geometry : angle 0.56691 (14000) *********************** 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 86 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4532 (mtt) cc_final: 0.3632 (mmt) REVERT: A 40 LEU cc_start: 0.9563 (mp) cc_final: 0.9304 (mm) REVERT: A 478 MET cc_start: 0.8249 (mmp) cc_final: 0.7902 (mmp) REVERT: A 484 TRP cc_start: 0.6633 (m-10) cc_final: 0.6362 (m-10) REVERT: A 500 GLU cc_start: 0.8845 (tt0) cc_final: 0.8353 (tt0) REVERT: A 515 MET cc_start: 0.8873 (tpt) cc_final: 0.8406 (tpt) REVERT: A 775 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (mp10) REVERT: C 154 ASP cc_start: 0.8368 (t70) cc_final: 0.7449 (t70) REVERT: C 225 ASN cc_start: 0.8735 (m110) cc_final: 0.8494 (t0) REVERT: C 242 LEU cc_start: 0.8551 (mp) cc_final: 0.8328 (mp) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 0.2164 time to fit residues: 27.5196 Evaluate side-chains 76 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP 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 311 ASP 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: 3.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.053502 restraints weight = 36248.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055597 restraints weight = 16810.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056965 restraints weight = 10243.829| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10366 Z= 0.123 Angle : 0.557 9.811 14006 Z= 0.277 Chirality : 0.041 0.176 1530 Planarity : 0.004 0.055 1785 Dihedral : 6.637 74.260 1403 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.93 % Allowed : 8.70 % Favored : 90.38 % 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: 1.93 (0.22), residues: 603 sheet: 1.28 (0.40), residues: 165 loop : 0.83 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.015 0.001 PHE A 360 TYR 0.018 0.001 TYR A 102 ARG 0.011 0.000 ARG B 110 Details of bonding type rmsd link_TRANS : bond 0.00202 ( 2) link_TRANS : angle 0.86123 ( 6) hydrogen bonds : bond 0.03360 ( 522) hydrogen bonds : angle 4.38497 ( 1464) covalent geometry : bond 0.00279 (10364) covalent geometry : angle 0.55684 (14000) *********************** 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: 10 poor density : 84 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6652 (ppp) cc_final: 0.6427 (tmm) REVERT: B 120 MET cc_start: 0.4604 (mtt) cc_final: 0.3858 (tpp) REVERT: A 40 LEU cc_start: 0.9541 (mp) cc_final: 0.9261 (mm) REVERT: A 478 MET cc_start: 0.8171 (mmp) cc_final: 0.7698 (mmm) REVERT: A 484 TRP cc_start: 0.6666 (m-10) cc_final: 0.6166 (m-10) REVERT: A 500 GLU cc_start: 0.8848 (tt0) cc_final: 0.8328 (tt0) REVERT: A 515 MET cc_start: 0.8728 (tpt) cc_final: 0.8322 (tpt) REVERT: C 154 ASP cc_start: 0.8340 (t70) cc_final: 0.7506 (t70) REVERT: C 225 ASN cc_start: 0.8700 (m110) cc_final: 0.8496 (t0) REVERT: C 242 LEU cc_start: 0.8518 (mp) cc_final: 0.8265 (mp) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.2213 time to fit residues: 30.5490 Evaluate side-chains 78 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.0010 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054125 restraints weight = 36348.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.056227 restraints weight = 16762.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057617 restraints weight = 10240.417| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10366 Z= 0.106 Angle : 0.562 8.169 14006 Z= 0.278 Chirality : 0.041 0.173 1530 Planarity : 0.004 0.056 1785 Dihedral : 6.303 67.841 1403 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.39 % Allowed : 8.97 % Favored : 89.64 % 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: 1.88 (0.22), residues: 609 sheet: 1.45 (0.40), residues: 159 loop : 0.82 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.006 0.001 HIS B 111 PHE 0.015 0.001 PHE A 360 TYR 0.015 0.001 TYR A 102 ARG 0.003 0.000 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.00193 ( 2) link_TRANS : angle 0.85755 ( 6) hydrogen bonds : bond 0.03268 ( 522) hydrogen bonds : angle 4.36555 ( 1464) covalent geometry : bond 0.00234 (10364) covalent geometry : angle 0.56218 (14000) *********************** 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 89 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9254 (ppt170) cc_final: 0.8931 (ppt170) REVERT: B 120 MET cc_start: 0.4453 (mtt) cc_final: 0.3722 (tpp) REVERT: A 40 LEU cc_start: 0.9536 (mp) cc_final: 0.9264 (mm) REVERT: A 354 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.8647 (t70) REVERT: A 478 MET cc_start: 0.8144 (mmp) cc_final: 0.7678 (mmm) REVERT: A 484 TRP cc_start: 0.6708 (m-10) cc_final: 0.6174 (m-10) REVERT: A 500 GLU cc_start: 0.8822 (tt0) cc_final: 0.8302 (tt0) REVERT: A 515 MET cc_start: 0.8685 (tpt) cc_final: 0.8348 (tpt) REVERT: A 775 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: C 225 ASN cc_start: 0.8682 (m110) cc_final: 0.8459 (t0) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.2105 time to fit residues: 28.1155 Evaluate side-chains 82 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.0170 chunk 22 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.054067 restraints weight = 36640.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056157 restraints weight = 16860.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057537 restraints weight = 10251.233| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10366 Z= 0.120 Angle : 0.562 9.583 14006 Z= 0.277 Chirality : 0.041 0.172 1530 Planarity : 0.004 0.055 1785 Dihedral : 6.112 67.525 1403 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.02 % Allowed : 9.71 % Favored : 89.27 % 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: 2.09 (0.25), residues: 1231 helix: 1.92 (0.21), residues: 609 sheet: 1.36 (0.41), residues: 165 loop : 0.82 (0.31), residues: 457 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 0.015 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.00204 ( 2) link_TRANS : angle 0.85831 ( 6) hydrogen bonds : bond 0.03322 ( 522) hydrogen bonds : angle 4.34559 ( 1464) covalent geometry : bond 0.00272 (10364) covalent geometry : angle 0.56150 (14000) *********************** 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 87 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9247 (ppt170) cc_final: 0.8869 (ppt170) REVERT: B 120 MET cc_start: 0.4542 (mtt) cc_final: 0.3985 (tpp) REVERT: A 40 LEU cc_start: 0.9524 (mp) cc_final: 0.9237 (mm) REVERT: A 354 HIS cc_start: 0.8889 (OUTLIER) cc_final: 0.8643 (t70) REVERT: A 500 GLU cc_start: 0.8833 (tt0) cc_final: 0.8305 (tt0) REVERT: C 225 ASN cc_start: 0.8692 (m110) cc_final: 0.8472 (t0) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.2018 time to fit residues: 26.2865 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 : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 HIS 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 145 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR 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: 0.6980 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.073510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053213 restraints weight = 36534.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055284 restraints weight = 16807.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056664 restraints weight = 10215.632| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10366 Z= 0.134 Angle : 0.573 8.391 14006 Z= 0.284 Chirality : 0.041 0.173 1530 Planarity : 0.004 0.054 1785 Dihedral : 6.042 67.205 1403 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.11 % Allowed : 9.99 % Favored : 88.90 % 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: 2.06 (0.25), residues: 1231 helix: 1.91 (0.21), residues: 609 sheet: 1.29 (0.42), residues: 159 loop : 0.81 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.015 0.001 PHE A 360 TYR 0.013 0.001 TYR A 102 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.00210 ( 2) link_TRANS : angle 0.85649 ( 6) hydrogen bonds : bond 0.03390 ( 522) hydrogen bonds : angle 4.38109 ( 1464) covalent geometry : bond 0.00307 (10364) covalent geometry : angle 0.57259 (14000) *********************** 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: 12 poor density : 76 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9263 (ppt170) cc_final: 0.8939 (ppt170) REVERT: B 120 MET cc_start: 0.4783 (mtt) cc_final: 0.4521 (mmt) REVERT: A 40 LEU cc_start: 0.9530 (mp) cc_final: 0.9253 (mm) REVERT: A 135 MET cc_start: 0.8663 (mmm) cc_final: 0.8365 (tpp) REVERT: A 354 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8606 (t70) REVERT: A 478 MET cc_start: 0.8550 (mmp) cc_final: 0.8209 (mmp) REVERT: A 484 TRP cc_start: 0.6932 (m-10) cc_final: 0.6698 (m100) REVERT: A 500 GLU cc_start: 0.8839 (tt0) cc_final: 0.8614 (tt0) REVERT: A 515 MET cc_start: 0.8896 (tpt) cc_final: 0.8546 (tpt) REVERT: A 775 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8456 (mp10) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.2098 time to fit residues: 28.1200 Evaluate side-chains 81 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 386 THR 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 145 SER Chi-restraints excluded: chain C residue 221 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 100 optimal weight: 0.0070 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.0270 chunk 43 optimal weight: 0.7980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.054366 restraints weight = 36174.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056467 restraints weight = 16679.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057845 restraints weight = 10116.393| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10366 Z= 0.105 Angle : 0.569 9.275 14006 Z= 0.279 Chirality : 0.040 0.175 1530 Planarity : 0.004 0.056 1785 Dihedral : 5.761 67.722 1403 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 2.16 (0.25), residues: 1231 helix: 2.00 (0.22), residues: 608 sheet: 1.35 (0.42), residues: 159 loop : 0.86 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.016 0.001 PHE A 360 TYR 0.013 0.001 TYR A 102 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.00195 ( 2) link_TRANS : angle 0.84387 ( 6) hydrogen bonds : bond 0.03108 ( 522) hydrogen bonds : angle 4.26651 ( 1464) covalent geometry : bond 0.00237 (10364) covalent geometry : angle 0.56878 (14000) *********************** 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 83 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9287 (ppt170) cc_final: 0.8932 (ppt170) REVERT: A 40 LEU cc_start: 0.9534 (mp) cc_final: 0.9265 (mm) REVERT: A 135 MET cc_start: 0.8656 (mmm) cc_final: 0.8367 (tpp) REVERT: A 354 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8660 (t70) REVERT: A 478 MET cc_start: 0.8361 (mmp) cc_final: 0.8137 (mmp) REVERT: A 500 GLU cc_start: 0.8821 (tt0) cc_final: 0.8357 (tt0) REVERT: A 515 MET cc_start: 0.8864 (tpt) cc_final: 0.8392 (tpt) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.2301 time to fit residues: 28.2399 Evaluate side-chains 78 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 145 SER 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: 0.6980 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.053894 restraints weight = 36484.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.055967 restraints weight = 16834.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057342 restraints weight = 10249.638| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10366 Z= 0.122 Angle : 0.583 10.302 14006 Z= 0.287 Chirality : 0.041 0.172 1530 Planarity : 0.004 0.054 1785 Dihedral : 5.726 67.577 1403 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.65 % Allowed : 10.82 % 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: 2.16 (0.25), residues: 1231 helix: 1.96 (0.22), residues: 608 sheet: 1.48 (0.41), residues: 165 loop : 0.85 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.018 0.001 PHE A 470 TYR 0.013 0.001 TYR A 102 ARG 0.008 0.000 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.00205 ( 2) link_TRANS : angle 0.84448 ( 6) hydrogen bonds : bond 0.03301 ( 522) hydrogen bonds : angle 4.30649 ( 1464) covalent geometry : bond 0.00281 (10364) covalent geometry : angle 0.58248 (14000) ********************** 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 78 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9247 (ppt170) cc_final: 0.8938 (ppt170) REVERT: B 120 MET cc_start: 0.5112 (mmt) cc_final: 0.4444 (mmt) REVERT: A 40 LEU cc_start: 0.9530 (mp) cc_final: 0.9245 (mm) REVERT: A 354 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8629 (t70) REVERT: A 500 GLU cc_start: 0.8809 (tt0) cc_final: 0.8358 (tt0) REVERT: A 515 MET cc_start: 0.8893 (tpt) cc_final: 0.8427 (tpt) REVERT: A 775 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: C 44 MET cc_start: 0.8712 (mtp) cc_final: 0.8277 (tpt) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.3314 time to fit residues: 39.5115 Evaluate side-chains 75 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 SER 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: 2.9990 chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.053658 restraints weight = 36249.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055700 restraints weight = 16875.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057055 restraints weight = 10359.089| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10366 Z= 0.131 Angle : 0.602 10.831 14006 Z= 0.297 Chirality : 0.041 0.187 1530 Planarity : 0.004 0.058 1785 Dihedral : 5.712 67.295 1403 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.93 % Allowed : 10.64 % Favored : 88.44 % 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: 2.17 (0.25), residues: 1231 helix: 1.96 (0.22), residues: 609 sheet: 1.53 (0.41), residues: 164 loop : 0.86 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.016 0.001 PHE A 470 TYR 0.013 0.001 TYR A 102 ARG 0.008 0.000 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.00207 ( 2) link_TRANS : angle 0.84613 ( 6) hydrogen bonds : bond 0.03432 ( 522) hydrogen bonds : angle 4.37430 ( 1464) covalent geometry : bond 0.00301 (10364) covalent geometry : angle 0.60233 (14000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4565.92 seconds wall clock time: 85 minutes 11.96 seconds (5111.96 seconds total)