Starting phenix.real_space_refine on Mon Jul 28 13:40:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pma_13526/07_2025/7pma_13526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pma_13526/07_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_13526/07_2025/7pma_13526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2025/7pma_13526.map" model { file = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2025/7pma_13526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.09, per 1000 atoms: 0.80 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: 3.20 Conformation dependent library (CDL) restraints added in 1.3 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: 1.13 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: 3.94 Time building geometry restraints manager: 3.57 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: 21.310 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.540 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.880 ------------------------------------------------------------------------------- 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 10282 Z= 0.216 Angle : 0.887 11.880 13893 Z= 0.516 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 Details of bonding type rmsd link_TRANS : bond 0.00886 ( 2) link_TRANS : angle 4.26422 ( 6) hydrogen bonds : bond 0.16761 ( 519) hydrogen bonds : angle 7.40991 ( 1479) covalent geometry : bond 0.00436 (10280) covalent geometry : angle 0.88298 (13887) *********************** 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 : 1.216 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: 0.2795 time to fit residues: 60.5498 Evaluate side-chains 90 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 = 0.067086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.047573 restraints weight = 45428.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049240 restraints weight = 22207.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050378 restraints weight = 13700.296| |-----------------------------------------------------------------------------| 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 0.043 10282 Z= 0.156 Angle : 0.709 11.270 13893 Z= 0.362 Chirality : 0.045 0.271 1517 Planarity : 0.004 0.044 1770 Dihedral : 10.149 168.367 1392 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.65 % Allowed : 6.07 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1218 helix: 1.01 (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 0.016 0.002 TRP C 356 HIS 0.008 0.001 HIS C 275 PHE 0.028 0.002 PHE A 360 TYR 0.016 0.002 TYR A 711 ARG 0.005 0.001 ARG C 95 Details of bonding type rmsd link_TRANS : bond 0.00261 ( 2) link_TRANS : angle 1.08514 ( 6) hydrogen bonds : bond 0.04428 ( 519) hydrogen bonds : angle 5.28491 ( 1479) covalent geometry : bond 0.00342 (10280) covalent geometry : angle 0.70914 (13887) *********************** 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 113 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.062 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: 0.7294 (tp40) cc_final: 0.7033 (tp-100) REVERT: A 305 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8167 (ptp) REVERT: C 217 CYS cc_start: 0.8682 (m) cc_final: 0.7909 (m) outliers start: 7 outliers final: 3 residues processed: 111 average time/residue: 0.2092 time to fit residues: 33.5625 Evaluate side-chains 86 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.0070 chunk 106 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.066651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047358 restraints weight = 45927.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049013 restraints weight = 22268.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050143 restraints weight = 13699.298| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10282 Z= 0.138 Angle : 0.635 10.759 13893 Z= 0.321 Chirality : 0.043 0.210 1517 Planarity : 0.004 0.042 1770 Dihedral : 9.375 178.362 1391 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.49 % Allowed : 7.10 % Favored : 91.41 % 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: 1.59 (0.23), residues: 1218 helix: 1.51 (0.22), residues: 597 sheet: 1.02 (0.39), residues: 165 loop : 0.64 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 356 HIS 0.004 0.001 HIS C 275 PHE 0.017 0.002 PHE A 360 TYR 0.009 0.001 TYR A 477 ARG 0.003 0.000 ARG C 95 Details of bonding type rmsd link_TRANS : bond 0.00241 ( 2) link_TRANS : angle 1.08059 ( 6) hydrogen bonds : bond 0.03986 ( 519) hydrogen bonds : angle 4.99389 ( 1479) covalent geometry : bond 0.00305 (10280) covalent geometry : angle 0.63491 (13887) *********************** 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 96 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8474 (m90) REVERT: C 78 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8376 (p0) REVERT: C 217 CYS cc_start: 0.8782 (m) cc_final: 0.8009 (m) REVERT: C 225 ASN cc_start: 0.8995 (m-40) cc_final: 0.8209 (t0) outliers start: 16 outliers final: 6 residues processed: 94 average time/residue: 0.2480 time to fit residues: 34.3040 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 418 HIS 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: 0.7980 chunk 82 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.066652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047427 restraints weight = 45227.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049073 restraints weight = 21978.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050164 restraints weight = 13549.590| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10282 Z= 0.129 Angle : 0.617 10.075 13893 Z= 0.309 Chirality : 0.042 0.199 1517 Planarity : 0.004 0.038 1770 Dihedral : 8.856 169.606 1391 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.12 % Allowed : 7.94 % Favored : 90.94 % 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: 1.74 (0.22), residues: 587 sheet: 1.13 (0.39), residues: 163 loop : 0.66 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 356 HIS 0.005 0.001 HIS C 275 PHE 0.024 0.001 PHE A 360 TYR 0.010 0.001 TYR A 658 ARG 0.004 0.000 ARG B 37 Details of bonding type rmsd link_TRANS : bond 0.00205 ( 2) link_TRANS : angle 1.00669 ( 6) hydrogen bonds : bond 0.03672 ( 519) hydrogen bonds : angle 4.89635 ( 1479) covalent geometry : bond 0.00291 (10280) covalent geometry : angle 0.61666 (13887) *********************** 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 96 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7725 (tp-100) REVERT: A 418 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8717 (m170) REVERT: A 520 ASP cc_start: 0.8352 (m-30) cc_final: 0.7957 (m-30) REVERT: C 72 GLU cc_start: 0.8500 (tt0) cc_final: 0.8242 (tt0) REVERT: C 132 MET cc_start: 0.9042 (tmm) cc_final: 0.8558 (tmm) REVERT: C 217 CYS cc_start: 0.8763 (m) cc_final: 0.7967 (m) REVERT: C 225 ASN cc_start: 0.8953 (m-40) cc_final: 0.8141 (t0) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.2533 time to fit residues: 35.2634 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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 418 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 115 optimal weight: 0.0470 chunk 37 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 681 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047372 restraints weight = 45637.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049051 restraints weight = 22034.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050158 restraints weight = 13511.715| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10282 Z= 0.124 Angle : 0.605 11.713 13893 Z= 0.296 Chirality : 0.042 0.223 1517 Planarity : 0.004 0.037 1770 Dihedral : 8.146 149.029 1391 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.31 % Allowed : 8.12 % Favored : 90.57 % 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: 1.81 (0.24), residues: 1218 helix: 1.75 (0.22), residues: 602 sheet: 1.07 (0.39), residues: 163 loop : 0.65 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 356 HIS 0.005 0.001 HIS C 275 PHE 0.031 0.001 PHE A 360 TYR 0.011 0.001 TYR A 658 ARG 0.004 0.000 ARG A 779 Details of bonding type rmsd link_TRANS : bond 0.00216 ( 2) link_TRANS : angle 0.93328 ( 6) hydrogen bonds : bond 0.03535 ( 519) hydrogen bonds : angle 4.77668 ( 1479) covalent geometry : bond 0.00278 (10280) covalent geometry : angle 0.60455 (13887) *********************** 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 97 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8680 (mp0) cc_final: 0.8396 (mp0) REVERT: A 135 MET cc_start: 0.8804 (mmm) cc_final: 0.8158 (mmm) REVERT: A 418 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8510 (m90) REVERT: A 477 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8495 (t80) REVERT: A 702 TRP cc_start: 0.8161 (t-100) cc_final: 0.7702 (t-100) REVERT: C 72 GLU cc_start: 0.8460 (tt0) cc_final: 0.8174 (tt0) REVERT: C 86 TRP cc_start: 0.9222 (m-10) cc_final: 0.9017 (m-10) REVERT: C 132 MET cc_start: 0.9042 (tmm) cc_final: 0.8589 (tmm) REVERT: C 217 CYS cc_start: 0.8883 (m) cc_final: 0.8207 (m) REVERT: C 225 ASN cc_start: 0.8938 (m-40) cc_final: 0.8163 (t0) outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 0.2935 time to fit residues: 43.3498 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 418 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3445 r_free = 0.3445 target = 0.066532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047247 restraints weight = 45763.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048918 restraints weight = 22098.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050062 restraints weight = 13576.370| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10282 Z= 0.121 Angle : 0.602 10.302 13893 Z= 0.293 Chirality : 0.041 0.239 1517 Planarity : 0.004 0.037 1770 Dihedral : 7.536 126.492 1391 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.77 % Allowed : 8.50 % Favored : 89.73 % 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: 1.87 (0.24), residues: 1218 helix: 1.84 (0.22), residues: 601 sheet: 1.01 (0.39), residues: 163 loop : 0.67 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.010 0.001 HIS A 418 PHE 0.030 0.001 PHE A 360 TYR 0.010 0.001 TYR A 284 ARG 0.003 0.000 ARG A 257 Details of bonding type rmsd link_TRANS : bond 0.00211 ( 2) link_TRANS : angle 0.89563 ( 6) hydrogen bonds : bond 0.03402 ( 519) hydrogen bonds : angle 4.72032 ( 1479) covalent geometry : bond 0.00273 (10280) covalent geometry : angle 0.60173 (13887) *********************** 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 96 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7810 (pp20) REVERT: A 477 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8467 (t80) REVERT: A 702 TRP cc_start: 0.8164 (t-100) cc_final: 0.7710 (t-100) REVERT: A 788 MET cc_start: -0.1020 (mmm) cc_final: -0.1294 (mmm) REVERT: C 72 GLU cc_start: 0.8459 (tt0) cc_final: 0.8160 (tt0) REVERT: C 86 TRP cc_start: 0.9136 (m-10) cc_final: 0.8925 (m-10) REVERT: C 132 MET cc_start: 0.9059 (tmm) cc_final: 0.8604 (tmm) REVERT: C 176 MET cc_start: 0.8320 (mmm) cc_final: 0.8106 (mmt) REVERT: C 217 CYS cc_start: 0.8916 (m) cc_final: 0.8241 (m) REVERT: C 225 ASN cc_start: 0.8916 (m-40) cc_final: 0.8157 (t0) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 0.2298 time to fit residues: 31.6373 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 442 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 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 = 0.3460 r_free = 0.3460 target = 0.067164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047748 restraints weight = 45886.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049450 restraints weight = 22086.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050571 restraints weight = 13554.874| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10282 Z= 0.109 Angle : 0.608 11.723 13893 Z= 0.294 Chirality : 0.041 0.229 1517 Planarity : 0.003 0.038 1770 Dihedral : 7.065 108.025 1391 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.21 % Allowed : 9.62 % Favored : 89.17 % 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: 1.93 (0.24), residues: 1218 helix: 1.91 (0.22), residues: 596 sheet: 1.01 (0.40), residues: 163 loop : 0.69 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 781 HIS 0.004 0.001 HIS C 275 PHE 0.029 0.001 PHE A 360 TYR 0.009 0.001 TYR A 284 ARG 0.007 0.000 ARG B 37 Details of bonding type rmsd link_TRANS : bond 0.00190 ( 2) link_TRANS : angle 0.86917 ( 6) hydrogen bonds : bond 0.03223 ( 519) hydrogen bonds : angle 4.69443 ( 1479) covalent geometry : bond 0.00244 (10280) covalent geometry : angle 0.60794 (13887) *********************** 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 89 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7922 (pp20) REVERT: A 477 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8469 (t80) REVERT: A 702 TRP cc_start: 0.8207 (t-100) cc_final: 0.7718 (t-100) REVERT: C 72 GLU cc_start: 0.8446 (tt0) cc_final: 0.8177 (tt0) REVERT: C 217 CYS cc_start: 0.8920 (m) cc_final: 0.8215 (m) REVERT: C 225 ASN cc_start: 0.8910 (m-40) cc_final: 0.8150 (t0) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.2035 time to fit residues: 27.0636 Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 442 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain C residue 64 ILE 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 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.067537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047951 restraints weight = 45797.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.049663 restraints weight = 22171.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050792 restraints weight = 13607.227| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10282 Z= 0.111 Angle : 0.620 11.669 13893 Z= 0.296 Chirality : 0.041 0.221 1517 Planarity : 0.004 0.039 1770 Dihedral : 6.929 105.342 1391 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.12 % Allowed : 9.34 % Favored : 89.54 % 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: 1.88 (0.24), residues: 1218 helix: 1.93 (0.22), residues: 596 sheet: 0.82 (0.39), residues: 162 loop : 0.64 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 781 HIS 0.004 0.001 HIS C 275 PHE 0.030 0.001 PHE A 360 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG A 257 Details of bonding type rmsd link_TRANS : bond 0.00197 ( 2) link_TRANS : angle 0.85370 ( 6) hydrogen bonds : bond 0.03149 ( 519) hydrogen bonds : angle 4.65875 ( 1479) covalent geometry : bond 0.00251 (10280) covalent geometry : angle 0.61999 (13887) *********************** 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 90 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.7831 (t70) REVERT: A 135 MET cc_start: 0.8740 (mmm) cc_final: 0.8259 (mmm) REVERT: A 477 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8469 (t80) REVERT: A 520 ASP cc_start: 0.8072 (m-30) cc_final: 0.7829 (m-30) REVERT: A 648 MET cc_start: 0.9142 (mmm) cc_final: 0.8743 (tpp) REVERT: A 702 TRP cc_start: 0.8217 (t-100) cc_final: 0.7724 (t-100) REVERT: C 72 GLU cc_start: 0.8467 (tt0) cc_final: 0.8181 (tt0) REVERT: C 176 MET cc_start: 0.8216 (mmm) cc_final: 0.7928 (mmt) REVERT: C 217 CYS cc_start: 0.8957 (m) cc_final: 0.8254 (m) REVERT: C 225 ASN cc_start: 0.8899 (m-40) cc_final: 0.8141 (t0) outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.2148 time to fit residues: 28.5010 Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 12 ASN Chi-restraints excluded: chain C residue 64 ILE 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: 3.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 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 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 = 0.3462 r_free = 0.3462 target = 0.067141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047467 restraints weight = 45809.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049157 restraints weight = 22353.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050242 restraints weight = 13826.647| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10282 Z= 0.131 Angle : 0.639 12.569 13893 Z= 0.305 Chirality : 0.041 0.185 1517 Planarity : 0.004 0.037 1770 Dihedral : 6.858 104.316 1391 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.03 % Allowed : 9.80 % Favored : 89.17 % 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: 1.84 (0.22), residues: 602 sheet: 0.83 (0.39), residues: 163 loop : 0.57 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 781 HIS 0.005 0.001 HIS C 275 PHE 0.029 0.001 PHE A 360 TYR 0.009 0.001 TYR A 259 ARG 0.005 0.000 ARG C 256 Details of bonding type rmsd link_TRANS : bond 0.00228 ( 2) link_TRANS : angle 0.85127 ( 6) hydrogen bonds : bond 0.03240 ( 519) hydrogen bonds : angle 4.67735 ( 1479) covalent geometry : bond 0.00303 (10280) covalent geometry : angle 0.63865 (13887) *********************** 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 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7689 (tt0) REVERT: A 135 MET cc_start: 0.8739 (mmm) cc_final: 0.8278 (mmm) REVERT: A 477 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8479 (t80) REVERT: A 702 TRP cc_start: 0.8179 (t-100) cc_final: 0.7702 (t-100) REVERT: C 72 GLU cc_start: 0.8428 (tt0) cc_final: 0.8156 (tt0) REVERT: C 119 MET cc_start: 0.9060 (ttp) cc_final: 0.8812 (ttm) REVERT: C 217 CYS cc_start: 0.8904 (m) cc_final: 0.8219 (m) REVERT: C 225 ASN cc_start: 0.8880 (m-40) cc_final: 0.8137 (t0) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.2216 time to fit residues: 26.2730 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 185 LEU 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: 8.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 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 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047696 restraints weight = 45806.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049389 restraints weight = 22158.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.050505 restraints weight = 13675.723| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10282 Z= 0.120 Angle : 0.636 12.787 13893 Z= 0.305 Chirality : 0.041 0.184 1517 Planarity : 0.004 0.037 1770 Dihedral : 6.699 100.280 1391 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.84 % Allowed : 10.27 % 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: 1.90 (0.24), residues: 1218 helix: 2.05 (0.22), residues: 590 sheet: 0.75 (0.39), residues: 163 loop : 0.54 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 781 HIS 0.005 0.001 HIS C 275 PHE 0.029 0.001 PHE A 360 TYR 0.012 0.001 TYR A 284 ARG 0.005 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00220 ( 2) link_TRANS : angle 0.84392 ( 6) hydrogen bonds : bond 0.03175 ( 519) hydrogen bonds : angle 4.63523 ( 1479) covalent geometry : bond 0.00278 (10280) covalent geometry : angle 0.63600 (13887) ********************** 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 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7489 (tt0) REVERT: A 135 MET cc_start: 0.8733 (mmm) cc_final: 0.8279 (mmm) REVERT: A 477 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8470 (t80) REVERT: A 520 ASP cc_start: 0.7975 (m-30) cc_final: 0.7769 (m-30) REVERT: A 702 TRP cc_start: 0.8176 (t-100) cc_final: 0.7688 (t-100) REVERT: C 72 GLU cc_start: 0.8438 (tt0) cc_final: 0.8155 (tt0) REVERT: C 217 CYS cc_start: 0.8952 (m) cc_final: 0.8266 (m) REVERT: C 225 ASN cc_start: 0.8885 (m-40) cc_final: 0.8144 (t0) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.2027 time to fit residues: 24.3298 Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 185 LEU 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: 3.9990 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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 = 0.3431 r_free = 0.3431 target = 0.065876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046246 restraints weight = 45853.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047916 restraints weight = 22456.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048997 restraints weight = 13922.116| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10282 Z= 0.177 Angle : 0.660 12.974 13893 Z= 0.320 Chirality : 0.042 0.185 1517 Planarity : 0.004 0.035 1770 Dihedral : 6.838 101.420 1391 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.93 % Allowed : 10.18 % 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: 1.73 (0.24), residues: 1218 helix: 1.87 (0.22), residues: 600 sheet: 0.68 (0.39), residues: 163 loop : 0.50 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 781 HIS 0.005 0.001 HIS C 275 PHE 0.028 0.001 PHE A 360 TYR 0.013 0.001 TYR A 284 ARG 0.004 0.000 ARG A 178 Details of bonding type rmsd link_TRANS : bond 0.00309 ( 2) link_TRANS : angle 0.85693 ( 6) hydrogen bonds : bond 0.03506 ( 519) hydrogen bonds : angle 4.75249 ( 1479) covalent geometry : bond 0.00402 (10280) covalent geometry : angle 0.65958 (13887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.78 seconds wall clock time: 73 minutes 5.34 seconds (4385.34 seconds total)