Starting phenix.real_space_refine on Mon Jul 28 15:43:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmc_13528/07_2025/7pmc_13528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmc_13528/07_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_13528/07_2025/7pmc_13528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2025/7pmc_13528.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2025/7pmc_13528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_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-5711/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: 6.98, per 1000 atoms: 0.69 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: 2.85 Conformation dependent library (CDL) restraints added in 1.7 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: 1.28 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: 3.58 Time building geometry restraints manager: 3.37 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: 0.010 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.770 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- 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 10356 Z= 0.381 Angle : 1.069 11.861 13993 Z= 0.624 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 Details of bonding type rmsd link_TRANS : bond 0.00934 ( 2) link_TRANS : angle 4.27402 ( 6) hydrogen bonds : bond 0.16861 ( 510) hydrogen bonds : angle 8.10511 ( 1413) covalent geometry : bond 0.00844 (10354) covalent geometry : angle 1.06510 (13987) *********************** 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 : 1.197 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: 0.2753 time to fit residues: 66.4881 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 : 1.205 ------------------------------------------------------------------------------- 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 = 0.075264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056097 restraints weight = 43355.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057872 restraints weight = 22150.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059069 restraints weight = 14202.257| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 10356 Z= 0.147 Angle : 0.677 7.619 13993 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 Details of bonding type rmsd link_TRANS : bond 0.00300 ( 2) link_TRANS : angle 1.46138 ( 6) hydrogen bonds : bond 0.03957 ( 510) hydrogen bonds : angle 5.54524 ( 1413) covalent geometry : bond 0.00321 (10354) covalent geometry : angle 0.67665 (13987) *********************** 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 : 1.177 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: 0.7112 (tt0) cc_final: 0.6788 (mt-10) REVERT: A 177 MET cc_start: 0.8232 (ppp) cc_final: 0.8023 (ppp) REVERT: C 305 MET cc_start: 0.8779 (mmt) cc_final: 0.8467 (tpt) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.2236 time to fit residues: 42.6898 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 : 1.186 ------------------------------------------------------------------------------- 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: 0.8980 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 A 743 GLN C 111 ASN C 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.075426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056448 restraints weight = 44169.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058289 restraints weight = 22307.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059465 restraints weight = 14057.506| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10356 Z= 0.119 Angle : 0.593 7.276 13993 Z= 0.305 Chirality : 0.042 0.173 1529 Planarity : 0.004 0.059 1783 Dihedral : 8.984 125.054 1401 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.48 % Allowed : 9.44 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1229 helix: 1.19 (0.21), residues: 605 sheet: 0.51 (0.41), residues: 160 loop : 0.40 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 Details of bonding type rmsd link_TRANS : bond 0.00233 ( 2) link_TRANS : angle 1.02612 ( 6) hydrogen bonds : bond 0.03273 ( 510) hydrogen bonds : angle 5.00292 ( 1413) covalent geometry : bond 0.00260 (10354) covalent geometry : angle 0.59308 (13987) *********************** 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 128 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6526 (pmm) cc_final: 0.5757 (mmt) REVERT: A 177 MET cc_start: 0.8159 (ppp) cc_final: 0.7922 (ppp) REVERT: A 477 TYR cc_start: 0.8844 (m-80) cc_final: 0.8294 (t80) REVERT: A 788 MET cc_start: -0.1654 (mtt) cc_final: -0.1858 (ptp) REVERT: C 225 ASN cc_start: 0.8781 (m-40) cc_final: 0.8539 (m110) REVERT: C 227 MET cc_start: 0.7901 (tpp) cc_final: 0.7627 (tmm) REVERT: C 305 MET cc_start: 0.8780 (mmt) cc_final: 0.8500 (tpt) outliers start: 16 outliers final: 8 residues processed: 124 average time/residue: 0.2126 time to fit residues: 38.3750 Evaluate side-chains 92 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 385 GLU 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: 0.8980 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 398 ASN A 464 GLN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.074602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.055362 restraints weight = 44322.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057184 restraints weight = 22975.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058274 restraints weight = 14697.650| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10356 Z= 0.129 Angle : 0.596 8.850 13993 Z= 0.303 Chirality : 0.042 0.169 1529 Planarity : 0.004 0.058 1783 Dihedral : 7.736 116.821 1401 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.94 % Allowed : 10.56 % Favored : 87.50 % 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: 1.27 (0.24), residues: 1229 helix: 1.40 (0.21), residues: 605 sheet: 0.43 (0.41), residues: 162 loop : 0.42 (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 0.001 PHE C 352 TYR 0.012 0.001 TYR A 259 ARG 0.002 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00247 ( 2) link_TRANS : angle 0.94060 ( 6) hydrogen bonds : bond 0.03287 ( 510) hydrogen bonds : angle 4.90166 ( 1413) covalent geometry : bond 0.00285 (10354) covalent geometry : angle 0.59589 (13987) *********************** 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 118 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6751 (pmm) cc_final: 0.5794 (mmt) REVERT: A 177 MET cc_start: 0.8178 (ppp) cc_final: 0.7906 (ppp) REVERT: A 477 TYR cc_start: 0.8858 (m-80) cc_final: 0.8389 (t80) REVERT: C 227 MET cc_start: 0.7980 (tpp) cc_final: 0.7638 (tmm) REVERT: C 305 MET cc_start: 0.8876 (mmt) cc_final: 0.8648 (tpt) outliers start: 21 outliers final: 13 residues processed: 113 average time/residue: 0.2297 time to fit residues: 37.0447 Evaluate side-chains 97 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 TYR 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: 1.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 191 ASN A 638 HIS A 705 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.072493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053390 restraints weight = 44395.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055117 restraints weight = 22999.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.056205 restraints weight = 14808.186| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10356 Z= 0.201 Angle : 0.632 8.548 13993 Z= 0.323 Chirality : 0.043 0.174 1529 Planarity : 0.004 0.056 1783 Dihedral : 7.730 111.715 1401 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.94 % Allowed : 10.37 % 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: 1.20 (0.24), residues: 1229 helix: 1.41 (0.21), residues: 600 sheet: 0.18 (0.41), residues: 164 loop : 0.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 414 HIS 0.008 0.001 HIS C 275 PHE 0.023 0.002 PHE A 360 TYR 0.017 0.001 TYR A 439 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00352 ( 2) link_TRANS : angle 0.94890 ( 6) hydrogen bonds : bond 0.03603 ( 510) hydrogen bonds : angle 4.99326 ( 1413) covalent geometry : bond 0.00445 (10354) covalent geometry : angle 0.63222 (13987) *********************** 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 107 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.7095 (m-10) REVERT: B 109 LEU cc_start: 0.8862 (mt) cc_final: 0.8443 (pp) REVERT: A 132 MET cc_start: 0.6857 (pmm) cc_final: 0.5881 (mmt) REVERT: A 477 TYR cc_start: 0.8866 (m-80) cc_final: 0.8472 (t80) REVERT: A 788 MET cc_start: -0.0983 (mtt) cc_final: -0.1192 (ptp) REVERT: C 61 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8442 (mmtm) REVERT: C 225 ASN cc_start: 0.8742 (m-40) cc_final: 0.8489 (m110) REVERT: C 227 MET cc_start: 0.7987 (tpp) cc_final: 0.7602 (tmm) outliers start: 21 outliers final: 17 residues processed: 101 average time/residue: 0.2692 time to fit residues: 39.6529 Evaluate side-chains 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR 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 439 TYR 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: 0.9980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 1 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3662 r_free = 0.3662 target = 0.074391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.055192 restraints weight = 44635.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057009 restraints weight = 22916.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058168 restraints weight = 14600.051| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10356 Z= 0.110 Angle : 0.579 7.970 13993 Z= 0.289 Chirality : 0.041 0.171 1529 Planarity : 0.004 0.053 1783 Dihedral : 7.232 110.271 1401 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.94 % Allowed : 11.39 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1229 helix: 1.57 (0.21), residues: 603 sheet: 0.26 (0.42), residues: 164 loop : 0.43 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 523 HIS 0.005 0.001 HIS C 275 PHE 0.023 0.001 PHE A 360 TYR 0.010 0.001 TYR C 91 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00237 ( 2) link_TRANS : angle 0.89016 ( 6) hydrogen bonds : bond 0.03101 ( 510) hydrogen bonds : angle 4.67240 ( 1413) covalent geometry : bond 0.00245 (10354) covalent geometry : angle 0.57925 (13987) *********************** 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 114 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.6692 (pmm) cc_final: 0.5557 (mmt) REVERT: A 477 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8464 (t80) REVERT: A 633 LYS cc_start: 0.8648 (pttt) cc_final: 0.8179 (pptt) REVERT: C 61 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8471 (mmtm) REVERT: C 132 MET cc_start: 0.8082 (tmm) cc_final: 0.7821 (tmm) REVERT: C 305 MET cc_start: 0.8858 (tpt) cc_final: 0.8563 (mmt) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 0.2829 time to fit residues: 43.6160 Evaluate side-chains 96 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 77 optimal weight: 0.3980 chunk 10 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 chunk 36 optimal weight: 0.0170 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS 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 = 0.3689 r_free = 0.3689 target = 0.075596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056728 restraints weight = 44102.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058511 restraints weight = 22504.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059663 restraints weight = 14290.041| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10356 Z= 0.100 Angle : 0.584 9.644 13993 Z= 0.286 Chirality : 0.040 0.167 1529 Planarity : 0.004 0.052 1783 Dihedral : 6.889 110.958 1401 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 1.44 (0.24), residues: 1229 helix: 1.69 (0.21), residues: 605 sheet: 0.31 (0.44), residues: 155 loop : 0.35 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.010 0.001 TYR C 91 ARG 0.004 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00220 ( 2) link_TRANS : angle 0.84551 ( 6) hydrogen bonds : bond 0.02949 ( 510) hydrogen bonds : angle 4.52021 ( 1413) covalent geometry : bond 0.00217 (10354) covalent geometry : angle 0.58341 (13987) *********************** 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 113 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: H 1 TRP cc_start: 0.8697 (m100) cc_final: 0.8272 (m100) REVERT: A 477 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8429 (t80) REVERT: A 500 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: A 633 LYS cc_start: 0.8607 (pttt) cc_final: 0.8139 (pptt) REVERT: C 61 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8480 (mmtm) REVERT: C 132 MET cc_start: 0.8034 (tmm) cc_final: 0.7830 (tmm) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.2787 time to fit residues: 44.5677 Evaluate side-chains 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 234 ILE 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 737 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: 0.6980 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.073646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054552 restraints weight = 44801.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056342 restraints weight = 23203.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.057466 restraints weight = 14853.821| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10356 Z= 0.142 Angle : 0.608 8.904 13993 Z= 0.301 Chirality : 0.041 0.174 1529 Planarity : 0.004 0.050 1783 Dihedral : 7.006 112.061 1401 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.76 % Allowed : 13.06 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1229 helix: 1.70 (0.22), residues: 603 sheet: 0.23 (0.43), residues: 156 loop : 0.33 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.019 0.001 PHE A 360 TYR 0.028 0.001 TYR A 10 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00283 ( 2) link_TRANS : angle 0.84673 ( 6) hydrogen bonds : bond 0.03202 ( 510) hydrogen bonds : angle 4.63596 ( 1413) covalent geometry : bond 0.00316 (10354) covalent geometry : angle 0.60833 (13987) *********************** 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 101 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.5031 (OUTLIER) cc_final: 0.3028 (m) REVERT: A 477 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8449 (t80) REVERT: A 633 LYS cc_start: 0.8631 (pttt) cc_final: 0.8274 (pttp) REVERT: C 14 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7328 (p) REVERT: C 61 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8492 (mmtm) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 0.2244 time to fit residues: 31.6749 Evaluate side-chains 94 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS A 130 GLN ** 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 = 0.3645 r_free = 0.3645 target = 0.073668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054590 restraints weight = 44342.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.056357 restraints weight = 23052.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057481 restraints weight = 14824.993| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10356 Z= 0.135 Angle : 0.623 9.678 13993 Z= 0.307 Chirality : 0.042 0.198 1529 Planarity : 0.004 0.051 1783 Dihedral : 6.991 112.461 1401 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.30 % Allowed : 13.89 % Favored : 84.81 % 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: 1.74 (0.22), residues: 602 sheet: 0.24 (0.44), residues: 156 loop : 0.29 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.020 0.001 PHE C 352 TYR 0.024 0.001 TYR A 10 ARG 0.007 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00275 ( 2) link_TRANS : angle 0.84622 ( 6) hydrogen bonds : bond 0.03187 ( 510) hydrogen bonds : angle 4.64690 ( 1413) covalent geometry : bond 0.00301 (10354) covalent geometry : angle 0.62240 (13987) *********************** 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 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.5119 (OUTLIER) cc_final: 0.3110 (m) REVERT: A 477 TYR cc_start: 0.8804 (m-80) cc_final: 0.8443 (t80) REVERT: A 633 LYS cc_start: 0.8627 (pttt) cc_final: 0.8069 (pptt) REVERT: C 14 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7165 (p) REVERT: C 61 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8522 (mmtm) outliers start: 14 outliers final: 11 residues processed: 97 average time/residue: 0.2088 time to fit residues: 29.8006 Evaluate side-chains 96 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET 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: 0.3980 chunk 96 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3659 r_free = 0.3659 target = 0.074169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055040 restraints weight = 44587.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056829 restraints weight = 23236.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057981 restraints weight = 14937.348| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10356 Z= 0.117 Angle : 0.621 10.658 13993 Z= 0.302 Chirality : 0.041 0.201 1529 Planarity : 0.004 0.050 1783 Dihedral : 6.847 115.570 1401 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 13.89 % Favored : 84.91 % 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: 1.46 (0.25), residues: 1229 helix: 1.74 (0.22), residues: 607 sheet: 0.35 (0.44), residues: 155 loop : 0.29 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.024 0.001 PHE C 352 TYR 0.024 0.001 TYR A 10 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00251 ( 2) link_TRANS : angle 0.83936 ( 6) hydrogen bonds : bond 0.03047 ( 510) hydrogen bonds : angle 4.56154 ( 1413) covalent geometry : bond 0.00263 (10354) covalent geometry : angle 0.62138 (13987) ********************** 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 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.5244 (OUTLIER) cc_final: 0.3244 (m) REVERT: A 477 TYR cc_start: 0.8848 (m-80) cc_final: 0.8408 (t80) REVERT: A 482 ILE cc_start: 0.8503 (tt) cc_final: 0.8013 (pt) REVERT: A 633 LYS cc_start: 0.8629 (pttt) cc_final: 0.8276 (pttp) REVERT: A 648 MET cc_start: 0.8311 (tpp) cc_final: 0.7881 (tpp) REVERT: A 652 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8147 (m110) REVERT: C 14 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7072 (p) REVERT: C 61 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8564 (mmtm) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.2155 time to fit residues: 30.5132 Evaluate side-chains 98 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 234 ILE 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 652 ASN Chi-restraints excluded: chain A residue 715 MET 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: 1.9990 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.0870 chunk 57 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.075239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056372 restraints weight = 43870.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058151 restraints weight = 22754.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059347 restraints weight = 14559.121| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10356 Z= 0.104 Angle : 0.606 10.231 13993 Z= 0.293 Chirality : 0.040 0.195 1529 Planarity : 0.004 0.050 1783 Dihedral : 6.643 124.313 1401 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 13.98 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1229 helix: 1.81 (0.22), residues: 610 sheet: 0.66 (0.44), residues: 160 loop : 0.36 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.020 0.001 PHE A 360 TYR 0.023 0.001 TYR A 10 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00227 ( 2) link_TRANS : angle 0.83040 ( 6) hydrogen bonds : bond 0.02888 ( 510) hydrogen bonds : angle 4.46527 ( 1413) covalent geometry : bond 0.00230 (10354) covalent geometry : angle 0.60633 (13987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3759.11 seconds wall clock time: 68 minutes 13.63 seconds (4093.63 seconds total)