Starting phenix.real_space_refine on Fri Aug 22 14:42:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmj_38479/08_2025/8xmj_38479.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmj_38479/08_2025/8xmj_38479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmj_38479/08_2025/8xmj_38479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmj_38479/08_2025/8xmj_38479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmj_38479/08_2025/8xmj_38479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmj_38479/08_2025/8xmj_38479.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.044 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 33 5.16 5 C 2749 2.51 5 N 737 2.21 5 O 787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4314 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2157 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 3 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 14, 'PHE:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 169 Chain: "A" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2009 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 2 Unresolved non-hydrogen bonds: 502 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 9, 'ASP:plan': 5, 'GLN:plan1': 8, 'ASN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 229 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {' ZN': 4, 'AV0': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2072 SG CYS B 433 39.059 22.179 32.214 1.00310.31 S ATOM 2151 SG CYS B 446 37.404 31.901 33.060 1.00299.95 S ATOM 2157 SG CYS B 447 41.647 33.496 32.330 1.00322.36 S ATOM 4113 SG CYS A 437 34.366 28.816 55.511 1.00298.15 S ATOM 2096 SG CYS B 437 31.600 26.539 24.243 1.00302.54 S ATOM 4088 SG CYS A 433 28.848 23.213 50.279 1.00314.84 S ATOM 4160 SG CYS A 446 26.929 34.236 46.685 1.00267.47 S ATOM 4166 SG CYS A 447 23.554 33.952 47.429 1.00298.94 S Time building chain proxies: 1.24, per 1000 atoms: 0.29 Number of scatterers: 4314 At special positions: 0 Unit cell: (59.904, 119.808, 72.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 33 16.00 O 787 8.00 N 737 7.00 C 2749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.05 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 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 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 141.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 437 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 413 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 408 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 387 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 370 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 433 " pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 447 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 446 " pdb=" ZN A 605 " pdb="ZN ZN A 605 " - pdb=" NE2 HIS A 43 " pdb="ZN ZN A 605 " - pdb=" NE2 HIS A 251 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 387 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 433 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 373 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 447 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 446 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 251 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" SG CYS A 437 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 408 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 413 " 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 65.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 8 through 33 Processing helix chain 'B' and resid 34 through 62 removed outlier: 4.090A pdb=" N LEU B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 242 through 272 removed outlier: 3.589A pdb=" N SER B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.913A pdb=" N PHE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 344 Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'A' and resid 12 through 33 Processing helix chain 'A' and resid 34 through 63 removed outlier: 4.265A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 112 through 133 removed outlier: 4.032A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 273 removed outlier: 5.315A pdb=" N LEU A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N HIS A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 309 through 315 removed outlier: 3.521A pdb=" N TYR A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 344 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.824A pdb=" N VAL A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 410 removed outlier: 3.974A pdb=" N HIS A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'B' and resid 366 through 378 removed outlier: 6.386A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 382 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR B 416 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 384 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN B 418 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 386 " --> pdb=" O GLN B 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 375 removed outlier: 6.126A pdb=" N ALA A 384 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLN A 418 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA A 386 " --> pdb=" O GLN A 418 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 969 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: 0.83 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 804 1.33 - 1.45: 1087 1.45 - 1.58: 2466 1.58 - 1.70: 0 1.70 - 1.83: 40 Bond restraints: 4397 Sorted by residual: bond pdb=" N ASP B 255 " pdb=" CA ASP B 255 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N HIS B 387 " pdb=" CA HIS B 387 " ideal model delta sigma weight residual 1.462 1.422 0.040 1.28e-02 6.10e+03 9.69e+00 bond pdb=" CAX Y01 A 606 " pdb=" OAF Y01 A 606 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" CB HIS B 387 " pdb=" CG HIS B 387 " ideal model delta sigma weight residual 1.497 1.455 0.042 1.40e-02 5.10e+03 8.81e+00 bond pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta sigma weight residual 1.527 1.476 0.050 1.75e-02 3.27e+03 8.27e+00 ... (remaining 4392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 5824 1.51 - 3.03: 188 3.03 - 4.54: 34 4.54 - 6.06: 10 6.06 - 7.57: 4 Bond angle restraints: 6060 Sorted by residual: angle pdb=" C ALA B 386 " pdb=" N HIS B 387 " pdb=" CA HIS B 387 " ideal model delta sigma weight residual 123.13 117.27 5.86 1.51e+00 4.39e-01 1.51e+01 angle pdb=" N HIS A 408 " pdb=" CA HIS A 408 " pdb=" C HIS A 408 " ideal model delta sigma weight residual 111.82 116.25 -4.43 1.16e+00 7.43e-01 1.46e+01 angle pdb=" N ARG A 438 " pdb=" CA ARG A 438 " pdb=" C ARG A 438 " ideal model delta sigma weight residual 110.41 114.88 -4.47 1.23e+00 6.61e-01 1.32e+01 angle pdb=" N ASP B 255 " pdb=" CA ASP B 255 " pdb=" C ASP B 255 " ideal model delta sigma weight residual 111.07 107.33 3.74 1.07e+00 8.73e-01 1.22e+01 angle pdb=" C HIS B 387 " pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta sigma weight residual 111.23 117.09 -5.86 1.68e+00 3.54e-01 1.21e+01 ... (remaining 6055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.95: 2518 25.95 - 51.90: 96 51.90 - 77.85: 34 77.85 - 103.79: 12 103.79 - 129.74: 37 Dihedral angle restraints: 2697 sinusoidal: 821 harmonic: 1876 Sorted by residual: dihedral pdb=" CB CYS A 276 " pdb=" SG CYS A 276 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual 93.00 163.36 -70.36 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS B 276 " pdb=" SG CYS B 276 " pdb=" SG CYS B 282 " pdb=" CB CYS B 282 " ideal model delta sinusoidal sigma weight residual -86.00 -28.63 -57.37 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CCD AV0 B 605 " pdb=" CCS AV0 B 605 " pdb=" OBZ AV0 B 605 " pdb=" CCW AV0 B 605 " ideal model delta sinusoidal sigma weight residual 59.29 -70.45 129.74 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 2694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 681 0.067 - 0.133: 75 0.133 - 0.200: 1 0.200 - 0.266: 3 0.266 - 0.333: 2 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA HIS A 408 " pdb=" N HIS A 408 " pdb=" C HIS A 408 " pdb=" CB HIS A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA HIS B 387 " pdb=" N HIS B 387 " pdb=" C HIS B 387 " pdb=" CB HIS B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA GLU B 371 " pdb=" N GLU B 371 " pdb=" C GLU B 371 " pdb=" CB GLU B 371 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 759 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 387 " 0.034 2.00e-02 2.50e+03 3.17e-02 1.51e+01 pdb=" CG HIS B 387 " -0.035 2.00e-02 2.50e+03 pdb=" ND1 HIS B 387 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 387 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 HIS B 387 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS B 387 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 251 " 0.023 2.00e-02 2.50e+03 2.94e-02 1.30e+01 pdb=" CG HIS B 251 " -0.014 2.00e-02 2.50e+03 pdb=" ND1 HIS B 251 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 251 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS B 251 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS B 251 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 408 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.18e+00 pdb=" CG HIS A 408 " 0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS A 408 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS A 408 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 408 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 408 " -0.000 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 43 2.53 - 3.12: 3609 3.12 - 3.71: 7154 3.71 - 4.31: 8013 4.31 - 4.90: 13096 Nonbonded interactions: 31915 Sorted by model distance: nonbonded pdb=" OD1 ASP B 255 " pdb="ZN ZN B 603 " model vdw 1.932 2.230 nonbonded pdb=" OD1 ASP B 47 " pdb="ZN ZN B 603 " model vdw 1.950 2.230 nonbonded pdb=" OE1 GLU A 420 " pdb="ZN ZN A 603 " model vdw 1.959 2.230 nonbonded pdb=" OD2 ASP A 47 " pdb="ZN ZN A 605 " model vdw 1.989 2.230 nonbonded pdb=" OD2 ASP A 255 " pdb="ZN ZN A 605 " model vdw 1.991 2.230 ... (remaining 31910 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 11 through 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 47 or (resid 48 and (name N or na \ me CA or name C or name O or name CB )) or resid 49 through 242 or (resid 243 th \ rough 246 and (name N or name CA or name C or name O or name CB )) or resid 247 \ through 273 or (resid 274 and (name N or name CA or name C or name O or name CB \ )) or resid 275 through 288 or (resid 289 and (name N or name CA or name C or na \ me O or name CB )) or resid 290 through 297 or (resid 298 and (name N or name CA \ or name C or name O or name CB )) or resid 305 through 310 or (resid 311 and (n \ ame N or name CA or name C or name O or name CB )) or resid 312 through 316 or ( \ resid 317 and (name N or name CA or name C or name O or name CB )) or resid 318 \ through 334 or (resid 335 and (name N or name CA or name C or name O or name CB \ )) or resid 336 or (resid 337 through 338 and (name N or name CA or name C or na \ me O or name CB )) or resid 339 through 356 or (resid 357 through 361 and (name \ N or name CA or name C or name O or name CB )) or resid 362 through 366 or (resi \ d 367 and (name N or name CA or name C or name O or name CB )) or resid 368 thro \ ugh 393 or (resid 394 through 396 and (name N or name CA or name C or name O or \ name CB )) or resid 397 through 422 or (resid 430 through 431 and (name N or nam \ e CA or name C or name O or name CB )) or resid 432 through 433 or (resid 434 th \ rough 436 and (name N or name CA or name C or name O or name CB )) or resid 437 \ through 601 or resid 603 through 604)) selection = (chain 'B' and ((resid 11 through 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 or (resid 19 through 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 or (resid 22 through 23 and (name N or na \ me CA or name C or name O or name CB )) or resid 24 through 25 or (resid 26 thro \ ugh 42 and (name N or name CA or name C or name O or name CB )) or resid 43 thro \ ugh 52 or (resid 53 through 55 and (name N or name CA or name C or name O or nam \ e CB )) or resid 56 through 58 or (resid 59 through 64 and (name N or name CA or \ name C or name O or name CB )) or resid 65 through 66 or (resid 67 through 69 a \ nd (name N or name CA or name C or name O or name CB )) or resid 70 or (resid 71 \ through 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 86 or (resid 87 and (name N or name CA or name C or name O or name CB ) \ ) or resid 88 through 92 or (resid 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 through 98 or (resid 99 through 103 and (name N or na \ me CA or name C or name O or name CB )) or resid 104 through 109 or (resid 110 t \ hrough 112 and (name N or name CA or name C or name O or name CB )) or resid 113 \ or (resid 114 through 117 and (name N or name CA or name C or name O or name CB \ )) or resid 118 or (resid 119 and (name N or name CA or name C or name O or nam \ e CB )) or resid 120 or (resid 121 through 122 and (name N or name CA or name C \ or name O or name CB )) or resid 123 through 126 or (resid 127 through 129 and ( \ name N or name CA or name C or name O or name CB )) or (resid 130 through 133 an \ d (name N or name CA or name C or name O or name CB )) or (resid 242 through 246 \ and (name N or name CA or name C or name O or name CB )) or resid 247 or (resid \ 248 through 250 and (name N or name CA or name C or name O or name CB )) or res \ id 251 through 259 or (resid 260 through 261 and (name N or name CA or name C or \ name O or name CB )) or resid 262 or (resid 263 and (name N or name CA or name \ C or name O or name CB )) or resid 264 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 or (resid 270 and (name N \ or name CA or name C or name O or name CB )) or resid 271 or (resid 272 and (na \ me N or name CA or name C or name O or name CB )) or resid 273 through 280 or (r \ esid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 t \ hrough 285 or (resid 286 and (name N or name CA or name C or name O or name CB ) \ ) or resid 287 through 290 or (resid 291 through 293 and (name N or name CA or n \ ame C or name O or name CB )) or resid 294 through 296 or (resid 297 through 308 \ and (name N or name CA or name C or name O or name CB )) or resid 309 through 3 \ 21 or (resid 322 through 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 329 or (resid 330 through 331 and (name N or name CA \ or name C or name O or name CB )) or resid 332 or (resid 333 and (name N or name \ CA or name C or name O or name CB )) or resid 334 through 343 or (resid 344 thr \ ough 345 and (name N or name CA or name C or name O or name CB )) or resid 346 o \ r (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 48 through 355 or (resid 356 through 361 and (name N or name CA or name C or nam \ e O or name CB )) or resid 362 through 388 or (resid 389 and (name N or name CA \ or name C or name O or name CB )) or resid 390 through 405 or (resid 406 and (na \ me N or name CA or name C or name O or name CB )) or resid 407 through 416 or (r \ esid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 t \ hrough 434 or (resid 435 through 436 and (name N or name CA or name C or name O \ or name CB )) or resid 437 through 443 or (resid 444 through 445 and (name N or \ name CA or name C or name O or name CB )) or resid 446 through 601 or resid 603 \ through 604)) } 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: 1.750 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.012 0.386 4420 Z= 0.437 Angle : 0.659 7.573 6064 Z= 0.352 Chirality : 0.046 0.333 762 Planarity : 0.004 0.034 775 Dihedral : 24.612 129.743 1463 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.35), residues: 634 helix: 2.87 (0.26), residues: 392 sheet: 0.13 (0.85), residues: 47 loop : -0.93 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.024 0.002 TYR A 396 PHE 0.020 0.001 PHE B 294 TRP 0.009 0.001 TRP B 74 HIS 0.037 0.003 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4397) covalent geometry : angle 0.65667 ( 6060) SS BOND : bond 0.01438 ( 2) SS BOND : angle 2.29604 ( 4) hydrogen bonds : bond 0.12058 ( 328) hydrogen bonds : angle 3.90757 ( 969) metal coordination : bond 0.16293 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 PHE cc_start: 0.9367 (t80) cc_final: 0.9157 (t80) REVERT: B 294 PHE cc_start: 0.9268 (t80) cc_final: 0.9051 (t80) REVERT: B 330 TYR cc_start: 0.7861 (t80) cc_final: 0.7378 (t80) REVERT: B 413 HIS cc_start: 0.8674 (m-70) cc_final: 0.8398 (m-70) REVERT: A 353 ILE cc_start: 0.9687 (mp) cc_final: 0.9407 (mp) REVERT: A 355 ASN cc_start: 0.9542 (t0) cc_final: 0.9102 (t0) REVERT: A 397 MET cc_start: 0.8758 (mmp) cc_final: 0.8520 (mmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0408 time to fit residues: 8.7902 Evaluate side-chains 124 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3817 r_free = 0.3817 target = 0.113649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084068 restraints weight = 12494.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086226 restraints weight = 8888.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.087774 restraints weight = 6993.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088886 restraints weight = 5893.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089586 restraints weight = 5215.044| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4420 Z= 0.235 Angle : 0.721 8.534 6064 Z= 0.353 Chirality : 0.045 0.267 762 Planarity : 0.004 0.032 775 Dihedral : 13.600 110.830 900 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.35), residues: 634 helix: 2.28 (0.26), residues: 397 sheet: -0.60 (0.74), residues: 47 loop : -0.89 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 76 TYR 0.010 0.001 TYR B 270 PHE 0.021 0.002 PHE A 407 TRP 0.013 0.002 TRP B 273 HIS 0.010 0.002 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 4397) covalent geometry : angle 0.72028 ( 6060) SS BOND : bond 0.00480 ( 2) SS BOND : angle 1.12216 ( 4) hydrogen bonds : bond 0.03890 ( 328) hydrogen bonds : angle 3.88423 ( 969) metal coordination : bond 0.01260 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 CYS cc_start: 0.8856 (p) cc_final: 0.8629 (p) REVERT: B 330 TYR cc_start: 0.7548 (t80) cc_final: 0.7101 (t80) REVERT: B 355 ASN cc_start: 0.9535 (m110) cc_final: 0.9322 (m110) REVERT: B 375 TRP cc_start: 0.9037 (p90) cc_final: 0.8773 (p90) REVERT: B 383 ILE cc_start: 0.9357 (mp) cc_final: 0.9065 (mp) REVERT: A 80 MET cc_start: 0.9321 (tmm) cc_final: 0.9031 (tmm) REVERT: A 109 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 355 ASN cc_start: 0.9358 (t0) cc_final: 0.8824 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0344 time to fit residues: 6.4718 Evaluate side-chains 108 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3815 r_free = 0.3815 target = 0.113495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084493 restraints weight = 12515.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086656 restraints weight = 8828.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088178 restraints weight = 6930.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089270 restraints weight = 5830.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089777 restraints weight = 5156.275| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4420 Z= 0.164 Angle : 0.596 5.738 6064 Z= 0.297 Chirality : 0.041 0.135 762 Planarity : 0.004 0.031 775 Dihedral : 10.701 99.840 900 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.35), residues: 634 helix: 2.42 (0.26), residues: 405 sheet: -0.88 (0.75), residues: 47 loop : -1.00 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 10 TYR 0.011 0.002 TYR B 306 PHE 0.018 0.002 PHE A 407 TRP 0.014 0.001 TRP A 74 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4397) covalent geometry : angle 0.59578 ( 6060) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.60380 ( 4) hydrogen bonds : bond 0.03417 ( 328) hydrogen bonds : angle 3.58976 ( 969) metal coordination : bond 0.00605 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 CYS cc_start: 0.8769 (p) cc_final: 0.8478 (p) REVERT: B 330 TYR cc_start: 0.7491 (t80) cc_final: 0.7040 (t80) REVERT: B 355 ASN cc_start: 0.9501 (m110) cc_final: 0.9287 (m110) REVERT: B 413 HIS cc_start: 0.8708 (m-70) cc_final: 0.8318 (m-70) REVERT: A 355 ASN cc_start: 0.9323 (t0) cc_final: 0.8776 (t0) REVERT: A 372 LEU cc_start: 0.9112 (tp) cc_final: 0.8879 (tt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0377 time to fit residues: 7.4403 Evaluate side-chains 114 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3848 r_free = 0.3848 target = 0.116632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.087572 restraints weight = 11994.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089843 restraints weight = 8348.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091432 restraints weight = 6490.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092492 restraints weight = 5437.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093313 restraints weight = 4804.173| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4420 Z= 0.107 Angle : 0.534 5.350 6064 Z= 0.266 Chirality : 0.041 0.150 762 Planarity : 0.003 0.030 775 Dihedral : 10.223 105.711 900 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.35), residues: 634 helix: 2.68 (0.26), residues: 410 sheet: -0.85 (0.76), residues: 47 loop : -0.93 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 76 TYR 0.009 0.001 TYR A 396 PHE 0.017 0.001 PHE A 407 TRP 0.009 0.001 TRP A 74 HIS 0.017 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4397) covalent geometry : angle 0.53187 ( 6060) SS BOND : bond 0.00080 ( 2) SS BOND : angle 1.91314 ( 4) hydrogen bonds : bond 0.02886 ( 328) hydrogen bonds : angle 3.26158 ( 969) metal coordination : bond 0.01002 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7540 (t80) cc_final: 0.7091 (t80) REVERT: B 413 HIS cc_start: 0.8733 (m-70) cc_final: 0.8294 (m-70) REVERT: A 337 LYS cc_start: 0.8906 (mttp) cc_final: 0.8655 (mtmm) REVERT: A 355 ASN cc_start: 0.9290 (t0) cc_final: 0.8705 (t0) REVERT: A 372 LEU cc_start: 0.9022 (tp) cc_final: 0.8704 (tt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0409 time to fit residues: 7.9683 Evaluate side-chains 118 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3868 r_free = 0.3868 target = 0.117106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088642 restraints weight = 11872.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090936 restraints weight = 8224.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.092594 restraints weight = 6360.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093419 restraints weight = 5299.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094454 restraints weight = 4764.932| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4420 Z= 0.101 Angle : 0.516 5.127 6064 Z= 0.258 Chirality : 0.040 0.118 762 Planarity : 0.003 0.030 775 Dihedral : 10.135 115.275 900 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.36), residues: 634 helix: 2.72 (0.26), residues: 410 sheet: -1.04 (0.76), residues: 47 loop : -0.93 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.009 0.001 TYR B 333 PHE 0.015 0.001 PHE A 407 TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 4397) covalent geometry : angle 0.51547 ( 6060) SS BOND : bond 0.00091 ( 2) SS BOND : angle 1.16436 ( 4) hydrogen bonds : bond 0.02749 ( 328) hydrogen bonds : angle 3.20342 ( 969) metal coordination : bond 0.00291 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7478 (t80) cc_final: 0.7065 (t80) REVERT: B 355 ASN cc_start: 0.9525 (m110) cc_final: 0.9202 (m110) REVERT: B 413 HIS cc_start: 0.8773 (m-70) cc_final: 0.8371 (m-70) REVERT: A 109 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 337 LYS cc_start: 0.8889 (mttp) cc_final: 0.8687 (mtmm) REVERT: A 355 ASN cc_start: 0.9299 (t0) cc_final: 0.8667 (t0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0358 time to fit residues: 7.3571 Evaluate side-chains 116 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3844 r_free = 0.3844 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086563 restraints weight = 12480.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088836 restraints weight = 8663.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090461 restraints weight = 6727.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091521 restraints weight = 5620.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092331 restraints weight = 4987.911| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.391 4420 Z= 0.232 Angle : 0.541 6.248 6064 Z= 0.271 Chirality : 0.040 0.127 762 Planarity : 0.004 0.031 775 Dihedral : 10.293 123.946 900 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.35), residues: 634 helix: 2.67 (0.26), residues: 410 sheet: -1.32 (0.76), residues: 46 loop : -0.93 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 10 TYR 0.011 0.001 TYR A 396 PHE 0.016 0.001 PHE A 407 TRP 0.007 0.001 TRP A 312 HIS 0.004 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4397) covalent geometry : angle 0.53856 ( 6060) SS BOND : bond 0.00267 ( 2) SS BOND : angle 1.89369 ( 4) hydrogen bonds : bond 0.02899 ( 328) hydrogen bonds : angle 3.27670 ( 969) metal coordination : bond 0.08542 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7568 (t80) cc_final: 0.7105 (t80) REVERT: B 413 HIS cc_start: 0.8780 (m-70) cc_final: 0.8368 (m-70) REVERT: A 337 LYS cc_start: 0.8951 (mttp) cc_final: 0.8748 (mtmm) REVERT: A 355 ASN cc_start: 0.9342 (t0) cc_final: 0.8710 (t0) REVERT: A 372 LEU cc_start: 0.9021 (tp) cc_final: 0.8702 (tt) REVERT: A 397 MET cc_start: 0.8311 (mmp) cc_final: 0.8097 (mmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0422 time to fit residues: 8.0950 Evaluate side-chains 113 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.0770 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3797 r_free = 0.3797 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083350 restraints weight = 12325.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085801 restraints weight = 8604.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087429 restraints weight = 6651.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088772 restraints weight = 5573.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.089500 restraints weight = 4855.246| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4420 Z= 0.125 Angle : 0.535 5.815 6064 Z= 0.271 Chirality : 0.040 0.121 762 Planarity : 0.003 0.031 775 Dihedral : 10.350 126.748 900 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.36), residues: 634 helix: 2.65 (0.26), residues: 411 sheet: -1.43 (0.76), residues: 46 loop : -0.91 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 76 TYR 0.005 0.001 TYR B 270 PHE 0.021 0.001 PHE A 407 TRP 0.007 0.001 TRP A 312 HIS 0.022 0.002 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4397) covalent geometry : angle 0.53292 ( 6060) SS BOND : bond 0.00102 ( 2) SS BOND : angle 1.68903 ( 4) hydrogen bonds : bond 0.02892 ( 328) hydrogen bonds : angle 3.19237 ( 969) metal coordination : bond 0.01742 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7657 (t80) cc_final: 0.7170 (t80) REVERT: B 376 GLN cc_start: 0.8605 (pp30) cc_final: 0.8356 (pp30) REVERT: B 377 LEU cc_start: 0.9245 (tp) cc_final: 0.8939 (tp) REVERT: B 413 HIS cc_start: 0.8808 (m-70) cc_final: 0.8470 (m90) REVERT: B 418 GLN cc_start: 0.9127 (tt0) cc_final: 0.8620 (tt0) REVERT: A 355 ASN cc_start: 0.9441 (t0) cc_final: 0.8811 (t0) REVERT: A 372 LEU cc_start: 0.8989 (tp) cc_final: 0.8729 (tt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0378 time to fit residues: 7.2411 Evaluate side-chains 115 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 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 = 0.3773 r_free = 0.3773 target = 0.109633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081646 restraints weight = 12799.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083704 restraints weight = 9116.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085170 restraints weight = 7216.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086107 restraints weight = 6107.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086884 restraints weight = 5461.812| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4420 Z= 0.282 Angle : 0.678 8.509 6064 Z= 0.359 Chirality : 0.042 0.137 762 Planarity : 0.004 0.034 775 Dihedral : 11.005 136.563 900 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.34), residues: 634 helix: 1.89 (0.25), residues: 397 sheet: -1.97 (0.71), residues: 47 loop : -1.04 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 76 TYR 0.017 0.002 TYR B 306 PHE 0.028 0.002 PHE A 407 TRP 0.019 0.002 TRP B 375 HIS 0.015 0.003 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 4397) covalent geometry : angle 0.67674 ( 6060) SS BOND : bond 0.00397 ( 2) SS BOND : angle 1.78180 ( 4) hydrogen bonds : bond 0.04109 ( 328) hydrogen bonds : angle 4.13390 ( 969) metal coordination : bond 0.01403 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.9114 (tmm) cc_final: 0.8873 (tmm) REVERT: B 330 TYR cc_start: 0.7573 (t80) cc_final: 0.7212 (t80) REVERT: B 376 GLN cc_start: 0.9080 (pp30) cc_final: 0.8774 (pp30) REVERT: A 355 ASN cc_start: 0.9353 (t0) cc_final: 0.8779 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0377 time to fit residues: 6.3881 Evaluate side-chains 97 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 0.0000 chunk 43 optimal weight: 0.0040 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 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 = 0.3840 r_free = 0.3840 target = 0.114602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086324 restraints weight = 12494.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088668 restraints weight = 8626.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090202 restraints weight = 6653.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091393 restraints weight = 5565.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091792 restraints weight = 4880.821| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4420 Z= 0.120 Angle : 0.568 6.910 6064 Z= 0.291 Chirality : 0.041 0.189 762 Planarity : 0.004 0.033 775 Dihedral : 10.675 134.532 900 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.35), residues: 634 helix: 2.48 (0.26), residues: 405 sheet: -1.77 (0.73), residues: 46 loop : -0.97 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 381 TYR 0.008 0.001 TYR B 330 PHE 0.021 0.001 PHE A 407 TRP 0.012 0.001 TRP B 74 HIS 0.015 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4397) covalent geometry : angle 0.56706 ( 6060) SS BOND : bond 0.00093 ( 2) SS BOND : angle 1.31496 ( 4) hydrogen bonds : bond 0.03072 ( 328) hydrogen bonds : angle 3.47320 ( 969) metal coordination : bond 0.01107 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7586 (t80) cc_final: 0.7088 (t80) REVERT: B 375 TRP cc_start: 0.8808 (p90) cc_final: 0.8588 (p90) REVERT: B 413 HIS cc_start: 0.8756 (m-70) cc_final: 0.8347 (m-70) REVERT: A 355 ASN cc_start: 0.9350 (t0) cc_final: 0.8762 (t0) REVERT: A 372 LEU cc_start: 0.8708 (tp) cc_final: 0.8461 (tt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0381 time to fit residues: 6.8739 Evaluate side-chains 113 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 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 = 0.3831 r_free = 0.3831 target = 0.113846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085604 restraints weight = 12511.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087886 restraints weight = 8692.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089440 restraints weight = 6744.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090487 restraints weight = 5636.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091327 restraints weight = 4989.456| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4420 Z= 0.137 Angle : 0.573 7.183 6064 Z= 0.294 Chirality : 0.041 0.150 762 Planarity : 0.004 0.034 775 Dihedral : 10.618 136.225 900 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.35), residues: 634 helix: 2.50 (0.26), residues: 405 sheet: -2.06 (0.72), residues: 46 loop : -0.97 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 76 TYR 0.039 0.002 TYR A 396 PHE 0.024 0.001 PHE A 407 TRP 0.011 0.001 TRP B 375 HIS 0.014 0.002 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4397) covalent geometry : angle 0.57174 ( 6060) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.30953 ( 4) hydrogen bonds : bond 0.03115 ( 328) hydrogen bonds : angle 3.45212 ( 969) metal coordination : bond 0.01024 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7542 (t80) cc_final: 0.7056 (t80) REVERT: B 375 TRP cc_start: 0.8927 (p90) cc_final: 0.8570 (p90) REVERT: B 413 HIS cc_start: 0.8715 (m-70) cc_final: 0.8322 (m-70) REVERT: A 355 ASN cc_start: 0.9326 (t0) cc_final: 0.8733 (t0) REVERT: A 372 LEU cc_start: 0.8768 (tp) cc_final: 0.8498 (tt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0437 time to fit residues: 7.8169 Evaluate side-chains 113 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 0.0070 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 40.0000 chunk 2 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 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 = 0.3837 r_free = 0.3837 target = 0.114402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085799 restraints weight = 12559.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088111 restraints weight = 8674.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089653 restraints weight = 6703.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090853 restraints weight = 5604.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091602 restraints weight = 4921.796| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4420 Z= 0.125 Angle : 0.558 6.246 6064 Z= 0.287 Chirality : 0.041 0.140 762 Planarity : 0.004 0.035 775 Dihedral : 10.561 136.331 900 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.36), residues: 634 helix: 2.58 (0.26), residues: 405 sheet: -2.07 (0.73), residues: 46 loop : -1.00 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 381 TYR 0.035 0.002 TYR A 396 PHE 0.022 0.001 PHE A 407 TRP 0.008 0.001 TRP B 375 HIS 0.013 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4397) covalent geometry : angle 0.55761 ( 6060) SS BOND : bond 0.00108 ( 2) SS BOND : angle 1.20870 ( 4) hydrogen bonds : bond 0.02987 ( 328) hydrogen bonds : angle 3.43466 ( 969) metal coordination : bond 0.00946 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 824.69 seconds wall clock time: 14 minutes 49.19 seconds (889.19 seconds total)