Starting phenix.real_space_refine on Fri Feb 14 16:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pma_13526/02_2025/7pma_13526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pma_13526/02_2025/7pma_13526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2025/7pma_13526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2025/7pma_13526.map" model { file = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2025/7pma_13526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2025/7pma_13526.cif" } resolution = 3.6 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 62 5.16 5 C 6412 2.51 5 N 1710 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10066 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: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5987 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.51, per 1000 atoms: 0.65 Number of scatterers: 10066 At special positions: 0 Unit cell: (102.82, 142.04, 149.46, 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 62 16.00 P 4 15.00 Mg 2 11.99 O 1876 8.00 N 1710 7.00 C 6412 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: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 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: 2352 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 55.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.054A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.701A 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 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.696A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.693A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.740A 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: 3.505A pdb=" N VAL A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.051A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.371A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.624A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.367A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.887A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.699A pdb=" N LYS A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 479 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.837A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.504A pdb=" N ILE A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.561A 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 removed outlier: 3.505A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.550A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.839A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.724A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 removed outlier: 4.053A pdb=" N SER A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.769A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.921A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.827A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.960A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.589A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.145A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.830A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.574A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.344A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.791A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.397A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.536A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 354' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.725A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.532A pdb=" N VAL B 65 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 17 removed outlier: 3.972A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 17 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.534A pdb=" N SER A 162 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.640A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.674A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 521 hydrogen bonds defined for protein. 1479 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: 3.65 Time building geometry restraints manager: 3.08 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: 1671 1.32 - 1.44: 2728 1.44 - 1.56: 5775 1.56 - 1.69: 6 1.69 - 1.81: 100 Bond restraints: 10280 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 3.73e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.64e+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 8.47e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.47e+00 ... (remaining 10275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13529 2.38 - 4.75: 295 4.75 - 7.13: 50 7.13 - 9.50: 7 9.50 - 11.88: 6 Bond angle restraints: 13887 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 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" C LYS A 668 " pdb=" N PHE A 669 " pdb=" CA PHE A 669 " ideal model delta sigma weight residual 122.48 130.29 -7.81 1.77e+00 3.19e-01 1.95e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.79 -4.79 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 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.28 4.12 1.00e+00 1.00e+00 1.70e+01 ... (remaining 13882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 6024 31.82 - 63.65: 128 63.65 - 95.47: 40 95.47 - 127.29: 3 127.29 - 159.12: 2 Dihedral angle restraints: 6197 sinusoidal: 2549 harmonic: 3648 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.12 -159.12 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.39 -135.39 1 2.00e+01 2.50e-03 4.11e+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 300.00 175.57 124.43 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1068 0.044 - 0.089: 300 0.089 - 0.133: 119 0.133 - 0.177: 21 0.177 - 0.222: 9 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CA TYR A 10 " pdb=" N TYR A 10 " pdb=" C TYR A 10 " pdb=" CB TYR A 10 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET A 478 " pdb=" N MET A 478 " pdb=" C MET A 478 " pdb=" CB MET A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CG LEU B 113 " pdb=" CB LEU B 113 " pdb=" CD1 LEU B 113 " pdb=" CD2 LEU B 113 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1514 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.111 9.50e-02 1.11e+02 6.47e-02 2.29e+01 pdb=" NE ARG A 248 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.022 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 4.41e-02 1.94e+01 pdb=" C THR C 89 " 0.076 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 A 231 " 0.233 9.50e-02 1.11e+02 1.08e-01 1.45e+01 pdb=" NE ARG A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " 0.025 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 12 2.37 - 3.00: 5465 3.00 - 3.63: 15172 3.63 - 4.27: 22395 4.27 - 4.90: 37952 Nonbonded interactions: 80996 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.060 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1901 " pdb=" O3B ADP A1902 " model vdw 2.155 2.170 nonbonded pdb=" O PHE A 698 " pdb=" NH1 ARG A 701 " model vdw 2.184 3.120 ... (remaining 80991 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: 1.740 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 10280 Z= 0.273 Angle : 0.883 11.880 13887 Z= 0.514 Chirality : 0.051 0.222 1517 Planarity : 0.008 0.108 1770 Dihedral : 15.928 159.118 3839 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: -1.07 (0.21), residues: 1218 helix: -1.28 (0.17), residues: 572 sheet: 0.60 (0.37), residues: 165 loop : -0.16 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 484 HIS 0.006 0.001 HIS B 132 PHE 0.029 0.002 PHE A 673 TYR 0.035 0.006 TYR A 113 ARG 0.080 0.012 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.8764 (pt) cc_final: 0.8528 (pt) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.2504 time to fit residues: 54.7239 Evaluate side-chains 89 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 264 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 395 HIS A 410 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 533 ASN A 642 ASN A 652 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047542 restraints weight = 45441.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049229 restraints weight = 22281.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050344 restraints weight = 13746.887| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10280 Z= 0.219 Angle : 0.707 10.787 13887 Z= 0.361 Chirality : 0.045 0.285 1517 Planarity : 0.004 0.043 1770 Dihedral : 10.157 167.732 1392 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.75 % Allowed : 6.16 % Favored : 93.09 % 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: 1.08 (0.23), residues: 1218 helix: 0.99 (0.20), residues: 592 sheet: 0.87 (0.38), residues: 166 loop : 0.52 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 356 HIS 0.003 0.001 HIS A 418 PHE 0.028 0.002 PHE A 360 TYR 0.016 0.001 TYR A 711 ARG 0.005 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7329 (tp40) cc_final: 0.7086 (tp-100) REVERT: A 305 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8128 (ptp) REVERT: A 705 GLN cc_start: 0.9068 (mp10) cc_final: 0.8862 (pm20) REVERT: C 217 CYS cc_start: 0.8670 (m) cc_final: 0.7902 (m) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.2252 time to fit residues: 36.6124 Evaluate side-chains 87 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.0770 chunk 106 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 418 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.067291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.048000 restraints weight = 46047.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049592 restraints weight = 22158.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050776 restraints weight = 13793.229| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10280 Z= 0.175 Angle : 0.630 10.827 13887 Z= 0.316 Chirality : 0.042 0.211 1517 Planarity : 0.004 0.043 1770 Dihedral : 9.340 177.414 1391 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.49 % Allowed : 7.28 % Favored : 91.22 % 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: 1.60 (0.23), residues: 1218 helix: 1.52 (0.21), residues: 597 sheet: 0.97 (0.39), residues: 164 loop : 0.65 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 484 HIS 0.003 0.001 HIS C 275 PHE 0.020 0.001 PHE A 360 TYR 0.012 0.001 TYR A 658 ARG 0.004 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLN cc_start: 0.8999 (mp10) cc_final: 0.8791 (pm20) REVERT: C 78 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8359 (p0) REVERT: C 217 CYS cc_start: 0.8745 (m) cc_final: 0.7946 (m) REVERT: C 225 ASN cc_start: 0.8974 (m-40) cc_final: 0.8181 (t0) outliers start: 16 outliers final: 6 residues processed: 95 average time/residue: 0.2392 time to fit residues: 33.1163 Evaluate side-chains 79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 0.0060 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.4714 ------------------------------------------------------------------------------- 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 418 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048127 restraints weight = 45402.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049803 restraints weight = 21938.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050941 restraints weight = 13485.141| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10280 Z= 0.169 Angle : 0.609 10.227 13887 Z= 0.304 Chirality : 0.042 0.204 1517 Planarity : 0.004 0.039 1770 Dihedral : 8.728 169.425 1391 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.93 % Allowed : 8.03 % Favored : 91.04 % 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: 1.79 (0.24), residues: 1218 helix: 1.73 (0.22), residues: 591 sheet: 1.13 (0.39), residues: 163 loop : 0.66 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 PHE 0.026 0.001 PHE A 360 TYR 0.010 0.001 TYR A 658 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8708 (mp0) cc_final: 0.8416 (mp0) REVERT: A 520 ASP cc_start: 0.8271 (m-30) cc_final: 0.7878 (m-30) REVERT: C 72 GLU cc_start: 0.8470 (tt0) cc_final: 0.8234 (tt0) REVERT: C 217 CYS cc_start: 0.8780 (m) cc_final: 0.7982 (m) REVERT: C 225 ASN cc_start: 0.8913 (m-40) cc_final: 0.8124 (t0) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.2305 time to fit residues: 31.9785 Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 96 optimal weight: 0.0670 chunk 66 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3455 r_free = 0.3455 target = 0.067003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047739 restraints weight = 45474.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049423 restraints weight = 22059.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050552 restraints weight = 13560.170| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 0.042 10280 Z= 0.179 Angle : 0.597 11.605 13887 Z= 0.293 Chirality : 0.042 0.210 1517 Planarity : 0.004 0.037 1770 Dihedral : 8.104 152.220 1391 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.59 % Allowed : 8.22 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1218 helix: 1.71 (0.22), residues: 602 sheet: 1.06 (0.39), residues: 163 loop : 0.66 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 86 HIS 0.005 0.001 HIS C 275 PHE 0.026 0.001 PHE A 360 TYR 0.011 0.001 TYR A 658 ARG 0.004 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8494 (t80) REVERT: C 72 GLU cc_start: 0.8471 (tt0) cc_final: 0.8192 (tt0) REVERT: C 217 CYS cc_start: 0.8916 (m) cc_final: 0.8275 (m) REVERT: C 225 ASN cc_start: 0.8925 (m-40) cc_final: 0.8158 (t0) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 0.2182 time to fit residues: 30.8721 Evaluate side-chains 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 681 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3418 r_free = 0.3418 target = 0.065424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046102 restraints weight = 46042.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047729 restraints weight = 22432.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048806 restraints weight = 13884.214| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10280 Z= 0.258 Angle : 0.635 10.263 13887 Z= 0.313 Chirality : 0.042 0.260 1517 Planarity : 0.004 0.035 1770 Dihedral : 7.706 135.223 1391 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.59 % Allowed : 8.40 % Favored : 90.01 % 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: 1.77 (0.24), residues: 1218 helix: 1.75 (0.22), residues: 601 sheet: 0.95 (0.39), residues: 163 loop : 0.65 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 86 HIS 0.007 0.001 HIS C 275 PHE 0.023 0.001 PHE A 360 TYR 0.009 0.001 TYR A 259 ARG 0.009 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8633 (mp0) cc_final: 0.8287 (mp0) REVERT: A 135 MET cc_start: 0.8880 (mmm) cc_final: 0.8268 (mmm) REVERT: A 442 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: A 477 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8475 (t80) REVERT: A 648 MET cc_start: 0.9154 (tpp) cc_final: 0.8863 (tpp) REVERT: A 702 TRP cc_start: 0.8215 (t-100) cc_final: 0.7740 (t-100) REVERT: A 788 MET cc_start: -0.0925 (mmm) cc_final: -0.1158 (mmm) REVERT: C 72 GLU cc_start: 0.8470 (tt0) cc_final: 0.8156 (tt0) REVERT: C 176 MET cc_start: 0.8349 (mmm) cc_final: 0.8135 (mmt) REVERT: C 217 CYS cc_start: 0.8937 (m) cc_final: 0.8266 (m) REVERT: C 225 ASN cc_start: 0.8968 (m-40) cc_final: 0.8184 (t0) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.2628 time to fit residues: 34.7673 Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.0030 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 455 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3439 r_free = 0.3439 target = 0.066278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046824 restraints weight = 45911.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048389 restraints weight = 22344.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.049536 restraints weight = 14035.873| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10280 Z= 0.184 Angle : 0.623 12.671 13887 Z= 0.301 Chirality : 0.041 0.218 1517 Planarity : 0.004 0.049 1770 Dihedral : 7.115 112.748 1391 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.31 % Allowed : 9.34 % Favored : 89.36 % 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: 1.78 (0.24), residues: 1218 helix: 1.79 (0.22), residues: 601 sheet: 0.88 (0.39), residues: 163 loop : 0.61 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 86 HIS 0.005 0.001 HIS C 275 PHE 0.025 0.001 PHE A 360 TYR 0.008 0.001 TYR A 259 ARG 0.011 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8852 (mmm) cc_final: 0.8267 (mmm) REVERT: A 477 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8487 (t80) REVERT: A 510 ASP cc_start: 0.8684 (m-30) cc_final: 0.8439 (m-30) REVERT: A 702 TRP cc_start: 0.8206 (t-100) cc_final: 0.7738 (t-100) REVERT: C 72 GLU cc_start: 0.8447 (tt0) cc_final: 0.8181 (tt0) REVERT: C 217 CYS cc_start: 0.8955 (m) cc_final: 0.8248 (m) REVERT: C 225 ASN cc_start: 0.8935 (m-40) cc_final: 0.8172 (t0) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.2144 time to fit residues: 28.1691 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 59 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046892 restraints weight = 46016.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048555 restraints weight = 22375.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049661 restraints weight = 13855.497| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10280 Z= 0.184 Angle : 0.627 13.647 13887 Z= 0.300 Chirality : 0.041 0.188 1517 Planarity : 0.004 0.038 1770 Dihedral : 6.828 101.033 1391 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.12 % Allowed : 9.80 % Favored : 89.08 % 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: 1.78 (0.24), residues: 1218 helix: 1.83 (0.22), residues: 602 sheet: 0.77 (0.39), residues: 163 loop : 0.60 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 781 HIS 0.005 0.001 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8830 (mmm) cc_final: 0.8283 (mmm) REVERT: A 477 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8517 (t80) REVERT: A 510 ASP cc_start: 0.8702 (m-30) cc_final: 0.8445 (m-30) REVERT: A 702 TRP cc_start: 0.8205 (t-100) cc_final: 0.7724 (t-100) REVERT: C 72 GLU cc_start: 0.8445 (tt0) cc_final: 0.8156 (tt0) REVERT: C 176 MET cc_start: 0.8222 (mmm) cc_final: 0.7931 (mmt) REVERT: C 217 CYS cc_start: 0.8955 (m) cc_final: 0.8242 (m) REVERT: C 225 ASN cc_start: 0.8915 (m-40) cc_final: 0.8169 (t0) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.2194 time to fit residues: 27.9324 Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 0.0040 chunk 114 optimal weight: 0.5980 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3475 r_free = 0.3475 target = 0.067717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047986 restraints weight = 45216.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049685 restraints weight = 21931.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050798 restraints weight = 13520.323| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10280 Z= 0.149 Angle : 0.611 11.162 13887 Z= 0.293 Chirality : 0.041 0.185 1517 Planarity : 0.004 0.038 1770 Dihedral : 6.399 83.488 1391 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.75 % Allowed : 10.18 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1218 helix: 1.85 (0.22), residues: 596 sheet: 0.79 (0.39), residues: 163 loop : 0.64 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 781 HIS 0.004 0.000 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.014 0.001 TYR A 284 ARG 0.003 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7792 (tt0) REVERT: A 30 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.7991 (t70) REVERT: A 135 MET cc_start: 0.8740 (mmm) cc_final: 0.8263 (mmm) REVERT: A 477 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 510 ASP cc_start: 0.8700 (m-30) cc_final: 0.8432 (m-30) REVERT: A 648 MET cc_start: 0.9124 (mmm) cc_final: 0.8762 (tpp) REVERT: A 702 TRP cc_start: 0.8162 (t-100) cc_final: 0.7693 (t-100) REVERT: C 72 GLU cc_start: 0.8429 (tt0) cc_final: 0.8147 (tt0) REVERT: C 217 CYS cc_start: 0.8932 (m) cc_final: 0.8220 (m) REVERT: C 225 ASN cc_start: 0.8887 (m-40) cc_final: 0.8150 (t0) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 0.2422 time to fit residues: 30.0991 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.067072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047416 restraints weight = 45845.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049111 restraints weight = 22356.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050228 restraints weight = 13840.955| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10280 Z= 0.179 Angle : 0.615 12.126 13887 Z= 0.294 Chirality : 0.041 0.182 1517 Planarity : 0.004 0.037 1770 Dihedral : 6.321 80.666 1391 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.75 % Allowed : 10.36 % Favored : 88.89 % 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: 1.84 (0.24), residues: 1218 helix: 1.97 (0.22), residues: 590 sheet: 0.74 (0.40), residues: 163 loop : 0.55 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 86 HIS 0.004 0.001 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.012 0.001 TYR A 284 ARG 0.005 0.000 ARG A 701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7458 (tt0) REVERT: A 135 MET cc_start: 0.8753 (mmm) cc_final: 0.8281 (mmm) REVERT: A 477 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8430 (t80) REVERT: A 510 ASP cc_start: 0.8738 (m-30) cc_final: 0.8474 (m-30) REVERT: A 648 MET cc_start: 0.9118 (mmm) cc_final: 0.8690 (tpp) REVERT: A 702 TRP cc_start: 0.8133 (t-100) cc_final: 0.7658 (t-100) REVERT: C 72 GLU cc_start: 0.8430 (tt0) cc_final: 0.8147 (tt0) REVERT: C 217 CYS cc_start: 0.8939 (m) cc_final: 0.8254 (m) REVERT: C 225 ASN cc_start: 0.8893 (m-40) cc_final: 0.8159 (t0) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.2137 time to fit residues: 26.4673 Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3462 r_free = 0.3462 target = 0.067206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047547 restraints weight = 45506.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049230 restraints weight = 22283.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050332 restraints weight = 13807.788| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 10280 Z= 0.272 Angle : 0.928 59.200 13887 Z= 0.525 Chirality : 0.047 0.851 1517 Planarity : 0.004 0.058 1770 Dihedral : 6.425 80.668 1391 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.81 % Favored : 98.11 % Rotamer: Outliers : 0.84 % Allowed : 10.08 % Favored : 89.08 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.82 (0.24), residues: 1218 helix: 1.96 (0.22), residues: 590 sheet: 0.70 (0.40), residues: 163 loop : 0.55 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 86 HIS 0.004 0.001 HIS C 275 PHE 0.025 0.001 PHE A 360 TYR 0.027 0.001 TYR B 29 ARG 0.005 0.000 ARG A 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3422.20 seconds wall clock time: 62 minutes 19.37 seconds (3739.37 seconds total)