Starting phenix.real_space_refine on Sun Dec 29 11:58:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmc_13528/12_2024/7pmc_13528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmc_13528/12_2024/7pmc_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_13528/12_2024/7pmc_13528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmc_13528/12_2024/7pmc_13528.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmc_13528/12_2024/7pmc_13528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmc_13528/12_2024/7pmc_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-5532/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: 6.56, per 1000 atoms: 0.65 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: 2.77 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: 1.28 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: 3.75 Time building geometry restraints manager: 3.06 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: 2.050 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: 0.080 Process input model: 26.500 Find NCS groups from input model: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- 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 : 1.296 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: 0.2850 time to fit residues: 68.8501 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 : 1.210 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8858 (tp) cc_final: 0.8472 (pp) REVERT: A 164 GLU cc_start: 0.6641 (tt0) cc_final: 0.6408 (mt-10) REVERT: C 305 MET cc_start: 0.7702 (mmt) cc_final: 0.7431 (tpt) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.2331 time to fit residues: 44.5653 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 : 1.208 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10354 Z= 0.178 Angle : 0.599 7.106 13987 Z= 0.309 Chirality : 0.042 0.179 1529 Planarity : 0.004 0.058 1783 Dihedral : 9.131 125.325 1401 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 9.54 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1229 helix: 1.13 (0.21), residues: 605 sheet: 0.49 (0.41), residues: 160 loop : 0.39 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.012 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 127 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 299 MET cc_start: 0.7338 (mmp) cc_final: 0.7073 (mmp) REVERT: C 305 MET cc_start: 0.7737 (mmt) cc_final: 0.7481 (tpt) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.2420 time to fit residues: 43.1165 Evaluate side-chains 93 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 202 ILE Chi-restraints excluded: chain A residue 234 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.0050 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10354 Z= 0.199 Angle : 0.606 8.809 13987 Z= 0.308 Chirality : 0.042 0.171 1529 Planarity : 0.004 0.058 1783 Dihedral : 7.901 118.849 1401 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.85 % Allowed : 10.65 % 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: 1.23 (0.24), residues: 1229 helix: 1.38 (0.21), residues: 605 sheet: 0.43 (0.41), residues: 161 loop : 0.39 (0.29), residues: 463 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 0.026 0.002 PHE C 352 TYR 0.012 0.001 TYR A 259 ARG 0.003 0.000 ARG B 64 *********************** 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 110 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 299 MET cc_start: 0.7336 (mmp) cc_final: 0.7072 (mmm) REVERT: C 305 MET cc_start: 0.7866 (mmt) cc_final: 0.7642 (tpt) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.2354 time to fit residues: 35.0870 Evaluate side-chains 93 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN A 191 ASN A 638 HIS A 705 GLN C 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10354 Z= 0.187 Angle : 0.584 8.734 13987 Z= 0.294 Chirality : 0.041 0.169 1529 Planarity : 0.004 0.056 1783 Dihedral : 7.477 112.307 1401 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.04 % Allowed : 10.83 % Favored : 87.13 % 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: 1.30 (0.24), residues: 1229 helix: 1.50 (0.21), residues: 604 sheet: 0.19 (0.43), residues: 155 loop : 0.44 (0.29), residues: 470 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 0.023 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 115 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.247 Fit side-chains REVERT: B 8 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7626 (tp-100) REVERT: B 109 LEU cc_start: 0.8791 (mt) cc_final: 0.8383 (pp) REVERT: A 132 MET cc_start: 0.6436 (pmm) cc_final: 0.5935 (mmt) REVERT: A 477 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.8037 (t80) REVERT: C 305 MET cc_start: 0.7894 (mmt) cc_final: 0.7675 (tpt) outliers start: 22 outliers final: 13 residues processed: 111 average time/residue: 0.2295 time to fit residues: 37.1482 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 : 1.330 ------------------------------------------------------------------------------- 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 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 500 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4210 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= 0.218 Angle : 0.617 8.613 13987 Z= 0.309 Chirality : 0.042 0.170 1529 Planarity : 0.004 0.051 1783 Dihedral : 7.388 111.009 1401 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.04 % Allowed : 11.20 % Favored : 86.76 % 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: 1.26 (0.24), residues: 1229 helix: 1.48 (0.21), residues: 601 sheet: 0.28 (0.42), residues: 162 loop : 0.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.028 0.001 PHE C 352 TYR 0.012 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 111 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: B 8 GLN cc_start: 0.7787 (tp-100) cc_final: 0.7556 (tp-100) REVERT: B 109 LEU cc_start: 0.8872 (mt) cc_final: 0.8422 (pp) REVERT: A 477 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 633 LYS cc_start: 0.8413 (pttt) cc_final: 0.8036 (pptt) outliers start: 22 outliers final: 19 residues processed: 106 average time/residue: 0.2183 time to fit residues: 33.8866 Evaluate side-chains 103 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 371 MET Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 TYR 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 13 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4404 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= 0.176 Angle : 0.593 9.577 13987 Z= 0.295 Chirality : 0.041 0.168 1529 Planarity : 0.004 0.051 1783 Dihedral : 7.132 110.525 1401 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.13 % Allowed : 12.31 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1229 helix: 1.58 (0.21), residues: 602 sheet: 0.21 (0.44), residues: 155 loop : 0.35 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.009 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 115 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.2609 (OUTLIER) cc_final: 0.1322 (m) REVERT: B 8 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7596 (tp40) REVERT: A 477 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 633 LYS cc_start: 0.8384 (pttt) cc_final: 0.8000 (pptt) REVERT: C 14 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7570 (p) outliers start: 23 outliers final: 14 residues processed: 108 average time/residue: 0.2381 time to fit residues: 37.5409 Evaluate side-chains 103 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 477 TYR 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 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 130 GLN A 149 GLN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10354 Z= 0.281 Angle : 0.651 8.887 13987 Z= 0.327 Chirality : 0.043 0.179 1529 Planarity : 0.004 0.051 1783 Dihedral : 7.385 110.020 1401 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.04 % Allowed : 12.87 % Favored : 85.09 % 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: 1.18 (0.24), residues: 1229 helix: 1.52 (0.21), residues: 601 sheet: -0.02 (0.42), residues: 167 loop : 0.27 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 PHE 0.025 0.002 PHE C 352 TYR 0.016 0.001 TYR A 439 ARG 0.004 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 106 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.3039 (OUTLIER) cc_final: 0.1728 (m) REVERT: A 177 MET cc_start: 0.7822 (ppp) cc_final: 0.7479 (ppp) REVERT: A 477 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.8003 (t80) REVERT: A 633 LYS cc_start: 0.8414 (pttt) cc_final: 0.8029 (pptt) REVERT: C 14 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (p) outliers start: 22 outliers final: 15 residues processed: 99 average time/residue: 0.2164 time to fit residues: 31.4122 Evaluate side-chains 100 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 477 TYR Chi-restraints excluded: chain A residue 484 TRP 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 112 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10354 Z= 0.183 Angle : 0.619 8.920 13987 Z= 0.304 Chirality : 0.041 0.172 1529 Planarity : 0.004 0.050 1783 Dihedral : 7.131 110.212 1401 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.85 % Allowed : 13.33 % 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: 1.28 (0.24), residues: 1229 helix: 1.63 (0.21), residues: 600 sheet: -0.07 (0.44), residues: 157 loop : 0.30 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 PHE 0.026 0.001 PHE C 352 TYR 0.009 0.001 TYR A 559 ARG 0.004 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 105 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.3019 (OUTLIER) cc_final: 0.1881 (m) REVERT: A 477 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 633 LYS cc_start: 0.8412 (pttt) cc_final: 0.8069 (pttp) REVERT: C 14 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7482 (p) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.2273 time to fit residues: 32.9393 Evaluate side-chains 100 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 135 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.0050 chunk 124 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4738 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= 0.165 Angle : 0.610 9.191 13987 Z= 0.298 Chirality : 0.041 0.168 1529 Planarity : 0.004 0.049 1783 Dihedral : 6.897 113.038 1401 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.94 % Allowed : 13.06 % Favored : 85.00 % 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: 1.70 (0.21), residues: 601 sheet: 0.23 (0.44), residues: 153 loop : 0.23 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 456 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 108 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: H 5 CYS cc_start: 0.3208 (OUTLIER) cc_final: 0.1938 (m) REVERT: A 177 MET cc_start: 0.7718 (ppp) cc_final: 0.7360 (ppp) REVERT: A 346 ASP cc_start: 0.8020 (t0) cc_final: 0.7660 (t70) REVERT: A 633 LYS cc_start: 0.8418 (pttt) cc_final: 0.8078 (pptt) REVERT: C 14 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7417 (p) outliers start: 21 outliers final: 16 residues processed: 101 average time/residue: 0.2234 time to fit residues: 33.0402 Evaluate side-chains 98 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 135 MET 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 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 A residue 788 MET 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 30 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.0000 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.0470 overall best weight: 1.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 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 = 0.3626 r_free = 0.3626 target = 0.072731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053706 restraints weight = 44202.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055438 restraints weight = 23037.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056583 restraints weight = 14842.259| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4703 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= 0.237 Angle : 0.639 9.173 13987 Z= 0.316 Chirality : 0.042 0.173 1529 Planarity : 0.004 0.050 1783 Dihedral : 7.064 116.627 1401 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.04 % Allowed : 13.15 % 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: 1.31 (0.24), residues: 1229 helix: 1.67 (0.21), residues: 599 sheet: 0.01 (0.42), residues: 165 loop : 0.27 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.027 0.002 PHE C 352 TYR 0.013 0.001 TYR A 559 ARG 0.004 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.19 seconds wall clock time: 39 minutes 0.88 seconds (2340.88 seconds total)