Starting phenix.real_space_refine on Fri Feb 14 17:56:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmc_13528/02_2025/7pmc_13528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmc_13528/02_2025/7pmc_13528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmc_13528/02_2025/7pmc_13528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmc_13528/02_2025/7pmc_13528.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmc_13528/02_2025/7pmc_13528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmc_13528/02_2025/7pmc_13528.cif" } resolution = 3.7 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 6457 2.51 5 N 1722 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 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: 10139 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: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6069 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 5 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 6.37, per 1000 atoms: 0.63 Number of scatterers: 10139 At special positions: 0 Unit cell: (111.3, 140.98, 144.16, 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 1891 8.00 N 1722 7.00 C 6457 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 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: 2372 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 16 sheets defined 55.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.309A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.779A 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 96 removed outlier: 4.007A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) 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 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.509A pdb=" N SER A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.930A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.793A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.587A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.586A pdb=" N VAL A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 removed outlier: 4.062A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.381A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.680A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.664A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.789A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.735A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.598A pdb=" N ASN A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 479 Processing helix chain 'A' and resid 483 through 487 removed outlier: 4.006A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.515A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.130A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.955A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 595 No H-bonds generated for 'chain 'A' and resid 594 through 595' Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.639A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 712 through 715 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.941A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.630A pdb=" N TYR A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.573A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.676A 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 128 removed outlier: 4.082A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 4.139A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.911A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.705A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.588A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.504A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.294A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.787A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.820A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.250A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.675A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 4.210A 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 12 through 15 removed outlier: 3.832A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 242 removed outlier: 3.774A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA8, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB1, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.671A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.179A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.721A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.547A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 512 hydrogen bonds defined for protein. 1413 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: 2.83 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: 1740 1.32 - 1.44: 2695 1.44 - 1.57: 5811 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10354 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.42e+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 8.61e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.464 0.061 2.10e-02 2.27e+03 8.57e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.58e+00 ... (remaining 10349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 13372 2.37 - 4.74: 541 4.74 - 7.12: 62 7.12 - 9.49: 8 9.49 - 11.86: 4 Bond angle restraints: 13987 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 121.70 109.84 11.86 1.80e+00 3.09e-01 4.34e+01 angle pdb=" C VAL A 720 " pdb=" N LEU A 721 " pdb=" CA LEU A 721 " ideal model delta sigma weight residual 121.85 130.82 -8.97 1.77e+00 3.19e-01 2.57e+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 122.40 118.25 4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 13982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 6097 33.59 - 67.18: 117 67.18 - 100.76: 28 100.76 - 134.35: 6 134.35 - 167.94: 1 Dihedral angle restraints: 6249 sinusoidal: 2571 harmonic: 3678 Sorted by residual: dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 107.94 -167.94 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 71.54 -131.54 1 2.00e+01 2.50e-03 3.99e+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 300.00 169.31 130.69 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 6246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 861 0.041 - 0.081: 413 0.081 - 0.122: 171 0.122 - 0.163: 63 0.163 - 0.203: 21 Chirality restraints: 1529 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 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 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 2.31 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 1526 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.139 9.50e-02 1.11e+02 8.14e-02 3.68e+01 pdb=" NE ARG A 248 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C THR C 89 " 0.078 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " -0.106 9.50e-02 1.11e+02 5.91e-02 1.69e+01 pdb=" NE ARG C 312 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.019 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 12 2.37 - 3.00: 5761 3.00 - 3.63: 15190 3.63 - 4.27: 22666 4.27 - 4.90: 38044 Nonbonded interactions: 81673 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 1.965 2.170 nonbonded pdb=" OH TYR C 218 " pdb=" OE2 GLU C 226 " model vdw 2.164 3.040 nonbonded pdb=" O LYS B 26 " pdb=" NH2 ARG B 64 " model vdw 2.190 3.120 ... (remaining 81668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.350 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.008 0.122 10354 Z= 0.548 Angle : 1.065 11.861 13987 Z= 0.622 Chirality : 0.060 0.203 1529 Planarity : 0.008 0.106 1783 Dihedral : 16.215 167.941 3871 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % 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: -1.41 (0.21), residues: 1229 helix: -1.52 (0.16), residues: 583 sheet: 0.23 (0.40), residues: 145 loop : -0.26 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 484 HIS 0.013 0.003 HIS B 147 PHE 0.043 0.004 PHE A 673 TYR 0.045 0.007 TYR B 89 ARG 0.102 0.010 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8846 (tp) cc_final: 0.8405 (pp) REVERT: B 116 LEU cc_start: 0.8707 (mt) cc_final: 0.8505 (mp) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.2729 time to fit residues: 66.0226 Evaluate side-chains 91 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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: 1.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 81 HIS A 156 ASN A 191 ASN A 264 GLN A 418 HIS A 430 HIS A 455 ASN A 464 GLN A 468 HIS C 121 GLN C 137 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056088 restraints weight = 43302.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057863 restraints weight = 22146.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059055 restraints weight = 14203.272| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10354 Z= 0.212 Angle : 0.677 7.619 13987 Z= 0.358 Chirality : 0.044 0.256 1529 Planarity : 0.005 0.065 1783 Dihedral : 10.714 132.021 1402 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.02 % Allowed : 7.22 % Favored : 91.76 % 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: 0.58 (0.23), residues: 1229 helix: 0.55 (0.20), residues: 597 sheet: 0.27 (0.38), residues: 171 loop : 0.48 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 781 HIS 0.011 0.001 HIS B 111 PHE 0.027 0.002 PHE A 360 TYR 0.016 0.002 TYR B 89 ARG 0.006 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8939 (tp) cc_final: 0.8548 (pp) REVERT: A 164 GLU cc_start: 0.7111 (tt0) cc_final: 0.6788 (mt-10) REVERT: A 177 MET cc_start: 0.8232 (ppp) cc_final: 0.8024 (ppp) REVERT: C 132 MET cc_start: 0.7922 (tmm) cc_final: 0.7719 (tmm) REVERT: C 305 MET cc_start: 0.8778 (mmt) cc_final: 0.8468 (tpt) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.2366 time to fit residues: 45.6743 Evaluate side-chains 92 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN C 111 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.056021 restraints weight = 44272.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057860 restraints weight = 22427.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059020 restraints weight = 14148.775| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10354 Z= 0.183 Angle : 0.597 7.195 13987 Z= 0.308 Chirality : 0.042 0.173 1529 Planarity : 0.004 0.059 1783 Dihedral : 8.992 125.203 1401 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 9.35 % Favored : 88.98 % 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: 1.07 (0.24), residues: 1229 helix: 1.16 (0.21), residues: 605 sheet: 0.44 (0.42), residues: 161 loop : 0.40 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 781 HIS 0.006 0.001 HIS C 275 PHE 0.024 0.002 PHE A 360 TYR 0.013 0.001 TYR C 91 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6537 (pmm) cc_final: 0.5763 (mmt) REVERT: A 177 MET cc_start: 0.8166 (ppp) cc_final: 0.7927 (ppp) REVERT: A 477 TYR cc_start: 0.8864 (m-80) cc_final: 0.8277 (t80) REVERT: C 225 ASN cc_start: 0.8801 (m-40) cc_final: 0.8560 (m110) REVERT: C 227 MET cc_start: 0.7888 (tpp) cc_final: 0.7583 (tmm) REVERT: C 305 MET cc_start: 0.8814 (mmt) cc_final: 0.8545 (tpt) outliers start: 18 outliers final: 8 residues processed: 120 average time/residue: 0.2230 time to fit residues: 38.8038 Evaluate side-chains 91 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN A 464 GLN C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.074093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054656 restraints weight = 44814.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056452 restraints weight = 23337.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057540 restraints weight = 15009.566| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10354 Z= 0.209 Angle : 0.601 8.524 13987 Z= 0.308 Chirality : 0.042 0.169 1529 Planarity : 0.004 0.058 1783 Dihedral : 7.871 118.108 1401 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 10.65 % Favored : 87.69 % 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: 1.23 (0.24), residues: 1229 helix: 1.36 (0.21), residues: 606 sheet: 0.41 (0.41), residues: 161 loop : 0.40 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.006 0.001 HIS C 275 PHE 0.026 0.002 PHE C 352 TYR 0.012 0.001 TYR A 259 ARG 0.002 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6762 (pmm) cc_final: 0.5867 (mmt) REVERT: A 177 MET cc_start: 0.8198 (ppp) cc_final: 0.7945 (ppp) REVERT: A 477 TYR cc_start: 0.8903 (m-80) cc_final: 0.8437 (t80) REVERT: C 227 MET cc_start: 0.7993 (tpp) cc_final: 0.7569 (tmm) REVERT: C 305 MET cc_start: 0.8904 (mmt) cc_final: 0.8688 (tpt) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.2317 time to fit residues: 34.4216 Evaluate side-chains 91 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN A 111 ASN A 191 ASN A 638 HIS A 705 GLN C 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.073829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054696 restraints weight = 44094.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056457 restraints weight = 22685.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057587 restraints weight = 14522.599| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10354 Z= 0.198 Angle : 0.583 8.836 13987 Z= 0.294 Chirality : 0.041 0.170 1529 Planarity : 0.004 0.057 1783 Dihedral : 7.480 111.629 1401 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.13 % Allowed : 10.28 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1229 helix: 1.48 (0.21), residues: 603 sheet: 0.34 (0.42), residues: 162 loop : 0.44 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 PHE 0.022 0.001 PHE A 360 TYR 0.010 0.001 TYR A 259 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8844 (mt) cc_final: 0.8455 (pp) REVERT: A 132 MET cc_start: 0.6823 (pmm) cc_final: 0.5848 (mmt) REVERT: A 477 TYR cc_start: 0.8858 (m-80) cc_final: 0.8534 (t80) REVERT: C 61 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8520 (mmtm) REVERT: C 225 ASN cc_start: 0.8706 (m-40) cc_final: 0.8450 (m110) outliers start: 23 outliers final: 19 residues processed: 107 average time/residue: 0.2169 time to fit residues: 33.5888 Evaluate side-chains 102 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 110 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.072737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053500 restraints weight = 44965.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055251 restraints weight = 23181.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.056364 restraints weight = 14838.209| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.004 0.039 10354 Z= 0.266 Angle : 0.629 8.861 13987 Z= 0.316 Chirality : 0.042 0.171 1529 Planarity : 0.004 0.057 1783 Dihedral : 7.491 110.656 1401 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.22 % Allowed : 11.57 % Favored : 86.20 % 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: 1.26 (0.24), residues: 1229 helix: 1.51 (0.21), residues: 600 sheet: 0.10 (0.41), residues: 166 loop : 0.39 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 PHE 0.030 0.002 PHE C 352 TYR 0.016 0.001 TYR A 439 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8796 (mt) cc_final: 0.8391 (pp) REVERT: A 132 MET cc_start: 0.6770 (pmm) cc_final: 0.5842 (mmt) REVERT: A 477 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8619 (t80) REVERT: A 633 LYS cc_start: 0.8666 (pttt) cc_final: 0.8194 (pptt) REVERT: C 14 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7626 (p) REVERT: C 61 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8512 (mmtm) REVERT: C 225 ASN cc_start: 0.8839 (m-40) cc_final: 0.8635 (m110) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.2257 time to fit residues: 33.3814 Evaluate side-chains 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.074044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054852 restraints weight = 44597.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056641 restraints weight = 22872.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057821 restraints weight = 14544.585| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10354 Z= 0.165 Angle : 0.582 9.618 13987 Z= 0.289 Chirality : 0.041 0.166 1529 Planarity : 0.004 0.052 1783 Dihedral : 7.153 109.878 1401 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.13 % Allowed : 11.85 % Favored : 86.02 % 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: 1.35 (0.24), residues: 1229 helix: 1.63 (0.21), residues: 602 sheet: 0.15 (0.43), residues: 155 loop : 0.35 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.024 0.001 PHE C 352 TYR 0.010 0.001 TYR C 91 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.4931 (OUTLIER) cc_final: 0.2936 (m) REVERT: A 132 MET cc_start: 0.6722 (pmm) cc_final: 0.5636 (mmt) REVERT: A 477 TYR cc_start: 0.8886 (m-80) cc_final: 0.8539 (t80) REVERT: A 633 LYS cc_start: 0.8659 (pttt) cc_final: 0.8168 (pptt) REVERT: A 783 MET cc_start: 0.7070 (mmp) cc_final: 0.6858 (mmp) REVERT: C 61 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8523 (mmtm) outliers start: 23 outliers final: 16 residues processed: 104 average time/residue: 0.2383 time to fit residues: 35.8712 Evaluate side-chains 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS A 111 ASN A 286 HIS C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055378 restraints weight = 44523.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057191 restraints weight = 22834.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058334 restraints weight = 14536.786| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10354 Z= 0.165 Angle : 0.587 9.056 13987 Z= 0.289 Chirality : 0.041 0.169 1529 Planarity : 0.004 0.050 1783 Dihedral : 7.008 111.167 1401 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.67 % Allowed : 12.69 % Favored : 85.65 % 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: 1.36 (0.24), residues: 1229 helix: 1.64 (0.21), residues: 603 sheet: 0.34 (0.45), residues: 153 loop : 0.27 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.024 0.001 PHE C 352 TYR 0.010 0.001 TYR A 259 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.5073 (OUTLIER) cc_final: 0.3055 (m) REVERT: A 132 MET cc_start: 0.6584 (pmm) cc_final: 0.5591 (mmt) REVERT: A 135 MET cc_start: 0.8168 (ttm) cc_final: 0.7920 (ttm) REVERT: A 477 TYR cc_start: 0.8842 (m-80) cc_final: 0.8531 (t80) REVERT: A 633 LYS cc_start: 0.8601 (pttt) cc_final: 0.8032 (pptt) REVERT: C 14 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7298 (p) REVERT: C 61 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8551 (mmtm) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.2294 time to fit residues: 35.8686 Evaluate side-chains 102 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054921 restraints weight = 44018.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056668 restraints weight = 22923.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057828 restraints weight = 14709.158| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10354 Z= 0.187 Angle : 0.614 10.437 13987 Z= 0.299 Chirality : 0.041 0.204 1529 Planarity : 0.004 0.050 1783 Dihedral : 6.962 111.880 1401 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.94 % Allowed : 12.31 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.24), residues: 1229 helix: 1.69 (0.21), residues: 603 sheet: 0.40 (0.43), residues: 161 loop : 0.29 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.023 0.001 PHE C 352 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.5139 (OUTLIER) cc_final: 0.3146 (m) REVERT: A 135 MET cc_start: 0.8307 (ttm) cc_final: 0.8076 (ttm) REVERT: A 177 MET cc_start: 0.8336 (ppp) cc_final: 0.8103 (ppp) REVERT: A 477 TYR cc_start: 0.8877 (m-80) cc_final: 0.8516 (t80) REVERT: A 633 LYS cc_start: 0.8617 (pttt) cc_final: 0.8057 (pptt) REVERT: C 14 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7211 (p) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.2322 time to fit residues: 34.6309 Evaluate side-chains 101 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN A 652 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.074139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055028 restraints weight = 44609.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056797 restraints weight = 23136.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057987 restraints weight = 14831.852| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10354 Z= 0.180 Angle : 0.624 9.402 13987 Z= 0.304 Chirality : 0.041 0.195 1529 Planarity : 0.004 0.050 1783 Dihedral : 6.875 114.080 1401 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.57 % Allowed : 12.59 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1229 helix: 1.75 (0.21), residues: 602 sheet: 0.23 (0.44), residues: 153 loop : 0.28 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.023 0.001 PHE C 352 TYR 0.010 0.001 TYR A 259 ARG 0.003 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.5236 (OUTLIER) cc_final: 0.3249 (m) REVERT: A 135 MET cc_start: 0.8237 (ttm) cc_final: 0.8011 (ttm) REVERT: A 477 TYR cc_start: 0.8844 (m-80) cc_final: 0.8434 (t80) REVERT: A 482 ILE cc_start: 0.8511 (tt) cc_final: 0.7922 (pt) REVERT: A 633 LYS cc_start: 0.8657 (pttt) cc_final: 0.8266 (pttp) REVERT: C 14 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7184 (p) REVERT: C 227 MET cc_start: 0.7746 (mmt) cc_final: 0.7537 (tmm) REVERT: C 305 MET cc_start: 0.8710 (tpt) cc_final: 0.8479 (tpp) outliers start: 17 outliers final: 12 residues processed: 101 average time/residue: 0.2300 time to fit residues: 33.8569 Evaluate side-chains 98 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 chunk 17 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.075446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056532 restraints weight = 43812.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058289 restraints weight = 22685.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059409 restraints weight = 14536.738| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10354 Z= 0.150 Angle : 0.612 9.964 13987 Z= 0.295 Chirality : 0.041 0.194 1529 Planarity : 0.004 0.050 1783 Dihedral : 6.639 120.884 1401 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.30 % Allowed : 13.06 % Favored : 85.65 % 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: 1.57 (0.24), residues: 1229 helix: 1.81 (0.21), residues: 605 sheet: 0.49 (0.43), residues: 160 loop : 0.34 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 484 HIS 0.005 0.001 HIS B 147 PHE 0.022 0.001 PHE B 93 TYR 0.009 0.001 TYR A 658 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: 3303.74 seconds wall clock time: 60 minutes 8.72 seconds (3608.72 seconds total)