Starting phenix.real_space_refine on Thu Mar 6 01:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmj_38479/03_2025/8xmj_38479.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmj_38479/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmj_38479/03_2025/8xmj_38479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmj_38479/03_2025/8xmj_38479.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmj_38479/03_2025/8xmj_38479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmj_38479/03_2025/8xmj_38479.cif" } resolution = 4.18 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= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 9} 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: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 9} 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: 3.34, per 1000 atoms: 0.77 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: 1.19 Conformation dependent library (CDL) restraints added in 551.0 milliseconds 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: 0.36 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: 1.12 Time building geometry restraints manager: 1.35 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 447 or resid 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 447 or resid 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: 1.250 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- 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 : 0.004 0.061 4397 Z= 0.256 Angle : 0.657 7.573 6060 Z= 0.351 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 (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: 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 TRP 0.009 0.001 TRP B 74 HIS 0.037 0.003 HIS B 251 PHE 0.020 0.001 PHE B 294 TYR 0.024 0.002 TYR A 396 ARG 0.002 0.000 ARG B 76 *********************** 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 : 0.457 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: 0.1061 time to fit residues: 22.2062 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 40.0000 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.117325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087042 restraints weight = 12197.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089351 restraints weight = 8619.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.091081 restraints weight = 6716.970| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4397 Z= 0.220 Angle : 0.656 8.770 6060 Z= 0.310 Chirality : 0.043 0.276 762 Planarity : 0.004 0.033 775 Dihedral : 12.928 110.781 900 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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 (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: 2.11 (0.35), residues: 634 helix: 2.57 (0.26), residues: 410 sheet: -0.35 (0.77), residues: 47 loop : -1.00 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 273 HIS 0.010 0.002 HIS A 413 PHE 0.018 0.002 PHE A 407 TYR 0.008 0.001 TYR B 306 ARG 0.003 0.001 ARG A 76 *********************** 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 142 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 PHE cc_start: 0.9392 (t80) cc_final: 0.9102 (t80) REVERT: B 321 CYS cc_start: 0.8861 (p) cc_final: 0.8640 (p) REVERT: B 330 TYR cc_start: 0.7536 (t80) cc_final: 0.7152 (t80) REVERT: B 355 ASN cc_start: 0.9524 (m110) cc_final: 0.9321 (m110) REVERT: B 413 HIS cc_start: 0.8640 (m-70) cc_final: 0.8371 (m-70) REVERT: A 80 MET cc_start: 0.9178 (tmm) cc_final: 0.8935 (tmm) REVERT: A 109 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 355 ASN cc_start: 0.9372 (t0) cc_final: 0.8819 (t0) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1036 time to fit residues: 20.5894 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 21 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089517 restraints weight = 12158.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091938 restraints weight = 8458.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093526 restraints weight = 6539.354| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4397 Z= 0.134 Angle : 0.540 6.074 6060 Z= 0.262 Chirality : 0.040 0.125 762 Planarity : 0.004 0.032 775 Dihedral : 9.957 101.900 900 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 2.29 (0.35), residues: 634 helix: 2.73 (0.26), residues: 410 sheet: -0.47 (0.79), residues: 46 loop : -0.93 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.003 0.001 HIS A 408 PHE 0.041 0.002 PHE A 407 TYR 0.009 0.001 TYR A 396 ARG 0.001 0.000 ARG A 76 *********************** 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 152 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 PHE cc_start: 0.9363 (t80) cc_final: 0.9081 (t80) REVERT: B 294 PHE cc_start: 0.9185 (t80) cc_final: 0.8932 (t80) REVERT: B 321 CYS cc_start: 0.8852 (p) cc_final: 0.8590 (p) REVERT: B 330 TYR cc_start: 0.7543 (t80) cc_final: 0.7174 (t80) REVERT: B 355 ASN cc_start: 0.9547 (m110) cc_final: 0.9310 (m110) REVERT: A 76 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8034 (mtp85) REVERT: A 80 MET cc_start: 0.9197 (tmm) cc_final: 0.8973 (tmm) REVERT: A 109 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 337 LYS cc_start: 0.8907 (mttp) cc_final: 0.8674 (mtmm) REVERT: A 355 ASN cc_start: 0.9370 (t0) cc_final: 0.8809 (t0) REVERT: A 397 MET cc_start: 0.8469 (mmp) cc_final: 0.8255 (mmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1406 time to fit residues: 28.9716 Evaluate side-chains 122 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.114382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084329 restraints weight = 12121.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086498 restraints weight = 8669.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088015 restraints weight = 6859.775| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4397 Z= 0.245 Angle : 0.589 8.318 6060 Z= 0.299 Chirality : 0.041 0.125 762 Planarity : 0.004 0.032 775 Dihedral : 10.596 116.923 900 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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 (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 (0.35), residues: 634 helix: 2.42 (0.26), residues: 405 sheet: -0.84 (0.74), residues: 47 loop : -0.97 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 273 HIS 0.008 0.002 HIS B 408 PHE 0.023 0.002 PHE A 407 TYR 0.009 0.001 TYR B 270 ARG 0.004 0.001 ARG A 76 *********************** 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 129 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 PHE cc_start: 0.9402 (t80) cc_final: 0.9099 (t80) REVERT: B 321 CYS cc_start: 0.8915 (p) cc_final: 0.8601 (p) REVERT: B 330 TYR cc_start: 0.7698 (t80) cc_final: 0.7193 (t80) REVERT: B 355 ASN cc_start: 0.9581 (m110) cc_final: 0.9359 (m-40) REVERT: B 375 TRP cc_start: 0.8960 (p90) cc_final: 0.8704 (p90) REVERT: B 383 ILE cc_start: 0.9297 (mp) cc_final: 0.9055 (mp) REVERT: B 413 HIS cc_start: 0.8790 (m-70) cc_final: 0.8416 (m90) REVERT: A 80 MET cc_start: 0.9315 (tmm) cc_final: 0.9041 (tmm) REVERT: A 326 CYS cc_start: 0.9077 (t) cc_final: 0.8839 (p) REVERT: A 337 LYS cc_start: 0.8995 (mttp) cc_final: 0.8759 (mttp) REVERT: A 355 ASN cc_start: 0.9371 (t0) cc_final: 0.8801 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1274 time to fit residues: 22.5030 Evaluate side-chains 107 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.115480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086768 restraints weight = 12157.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.088969 restraints weight = 8540.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090552 restraints weight = 6679.647| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4397 Z= 0.179 Angle : 0.541 5.625 6060 Z= 0.274 Chirality : 0.041 0.129 762 Planarity : 0.004 0.032 775 Dihedral : 10.365 117.512 900 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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 (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: 2.09 (0.35), residues: 634 helix: 2.56 (0.26), residues: 410 sheet: -0.89 (0.76), residues: 47 loop : -0.85 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.019 0.002 HIS A 413 PHE 0.026 0.002 PHE A 407 TYR 0.006 0.001 TYR B 330 ARG 0.003 0.001 ARG A 76 *********************** 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 135 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7594 (t80) cc_final: 0.7122 (t80) REVERT: B 377 LEU cc_start: 0.9196 (tp) cc_final: 0.8954 (tp) REVERT: B 413 HIS cc_start: 0.8815 (m-70) cc_final: 0.8390 (m-70) REVERT: A 80 MET cc_start: 0.9202 (tmm) cc_final: 0.8996 (tmm) REVERT: A 337 LYS cc_start: 0.8953 (mttp) cc_final: 0.8742 (mtmm) REVERT: A 355 ASN cc_start: 0.9341 (t0) cc_final: 0.8740 (t0) REVERT: A 407 PHE cc_start: 0.9187 (m-80) cc_final: 0.8883 (m-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1743 time to fit residues: 32.4789 Evaluate side-chains 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** 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** ** 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 = 0.3830 r_free = 0.3830 target = 0.114451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085212 restraints weight = 12060.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087334 restraints weight = 8552.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088859 restraints weight = 6741.353| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4397 Z= 0.218 Angle : 0.560 6.821 6060 Z= 0.284 Chirality : 0.041 0.128 762 Planarity : 0.004 0.032 775 Dihedral : 10.352 124.498 900 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.49 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 (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 (0.35), residues: 634 helix: 2.50 (0.26), residues: 406 sheet: -1.21 (0.75), residues: 47 loop : -0.92 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 375 HIS 0.003 0.001 HIS A 373 PHE 0.020 0.002 PHE A 407 TYR 0.013 0.001 TYR A 396 ARG 0.005 0.001 ARG A 76 *********************** 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 134 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7654 (t80) cc_final: 0.7151 (t80) REVERT: B 375 TRP cc_start: 0.9330 (p90) cc_final: 0.8881 (p90) REVERT: B 413 HIS cc_start: 0.8783 (m-70) cc_final: 0.8400 (m-70) REVERT: A 80 MET cc_start: 0.9161 (tmm) cc_final: 0.8880 (tmm) REVERT: A 337 LYS cc_start: 0.8988 (mttp) cc_final: 0.8760 (mtmm) REVERT: A 355 ASN cc_start: 0.9308 (t0) cc_final: 0.8731 (t0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1197 time to fit residues: 22.0680 Evaluate side-chains 107 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.112998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082748 restraints weight = 11978.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085040 restraints weight = 8394.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086728 restraints weight = 6553.725| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4397 Z= 0.185 Angle : 0.540 5.900 6060 Z= 0.275 Chirality : 0.041 0.132 762 Planarity : 0.004 0.032 775 Dihedral : 10.417 127.153 900 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % 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 (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: 2.03 (0.35), residues: 634 helix: 2.59 (0.26), residues: 405 sheet: -1.26 (0.78), residues: 46 loop : -0.86 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 312 HIS 0.023 0.002 HIS A 413 PHE 0.023 0.002 PHE A 407 TYR 0.010 0.001 TYR A 396 ARG 0.004 0.001 ARG A 76 *********************** 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 134 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7718 (t80) cc_final: 0.7172 (t80) REVERT: B 375 TRP cc_start: 0.9126 (p90) cc_final: 0.8814 (p90) REVERT: B 413 HIS cc_start: 0.8831 (m-70) cc_final: 0.8444 (m-70) REVERT: A 80 MET cc_start: 0.9389 (tmm) cc_final: 0.8958 (tmm) REVERT: A 355 ASN cc_start: 0.9451 (t0) cc_final: 0.8830 (t0) REVERT: A 397 MET cc_start: 0.8569 (mmp) cc_final: 0.8306 (mmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0994 time to fit residues: 18.5463 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 : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 51 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.0570 chunk 63 optimal weight: 20.0000 overall best weight: 0.5020 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.117451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088923 restraints weight = 12118.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091356 restraints weight = 8404.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.092959 restraints weight = 6488.692| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4397 Z= 0.130 Angle : 0.522 7.094 6060 Z= 0.259 Chirality : 0.040 0.125 762 Planarity : 0.003 0.031 775 Dihedral : 10.226 129.066 900 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.36), residues: 634 helix: 2.77 (0.26), residues: 411 sheet: -1.25 (0.77), residues: 46 loop : -0.89 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.018 0.001 HIS A 413 PHE 0.015 0.001 PHE A 407 TYR 0.005 0.001 TYR B 330 ARG 0.004 0.001 ARG A 76 *********************** 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 142 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7549 (t80) cc_final: 0.7094 (t80) REVERT: B 375 TRP cc_start: 0.9200 (p90) cc_final: 0.8699 (p90) REVERT: B 376 GLN cc_start: 0.8898 (pp30) cc_final: 0.8677 (pp30) REVERT: B 413 HIS cc_start: 0.8845 (m-70) cc_final: 0.8424 (m-70) REVERT: B 418 GLN cc_start: 0.9390 (tt0) cc_final: 0.8825 (tt0) REVERT: A 80 MET cc_start: 0.9103 (tmm) cc_final: 0.8798 (tmm) REVERT: A 355 ASN cc_start: 0.9336 (t0) cc_final: 0.8703 (t0) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0962 time to fit residues: 19.2777 Evaluate side-chains 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 13 optimal weight: 5.9990 chunk 61 optimal weight: 0.0000 chunk 44 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.112419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082278 restraints weight = 12511.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084698 restraints weight = 8583.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086440 restraints weight = 6570.025| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4397 Z= 0.207 Angle : 0.558 6.088 6060 Z= 0.287 Chirality : 0.041 0.193 762 Planarity : 0.004 0.036 775 Dihedral : 10.559 134.586 900 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.32 % 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 (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: 1.99 (0.35), residues: 634 helix: 2.60 (0.26), residues: 411 sheet: -1.57 (0.72), residues: 47 loop : -1.04 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 375 HIS 0.004 0.001 HIS B 373 PHE 0.022 0.001 PHE A 407 TYR 0.018 0.001 TYR A 396 ARG 0.004 0.001 ARG A 76 *********************** 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 135 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7685 (t80) cc_final: 0.7140 (t80) REVERT: B 375 TRP cc_start: 0.9346 (p90) cc_final: 0.8886 (p90) REVERT: B 413 HIS cc_start: 0.8822 (m-70) cc_final: 0.8438 (m-70) REVERT: A 80 MET cc_start: 0.9402 (tmm) cc_final: 0.8962 (tmm) REVERT: A 326 CYS cc_start: 0.9148 (t) cc_final: 0.8900 (p) REVERT: A 355 ASN cc_start: 0.9425 (t0) cc_final: 0.8794 (t0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1057 time to fit residues: 19.8300 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 : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** A 418 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.115502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.086936 restraints weight = 12362.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089282 restraints weight = 8631.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090818 restraints weight = 6690.765| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4397 Z= 0.168 Angle : 0.540 6.240 6060 Z= 0.275 Chirality : 0.039 0.134 762 Planarity : 0.004 0.046 775 Dihedral : 10.484 133.233 900 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % 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 (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: 2.06 (0.36), residues: 634 helix: 2.66 (0.26), residues: 411 sheet: -1.68 (0.73), residues: 47 loop : -0.96 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.029 0.002 HIS A 413 PHE 0.024 0.001 PHE A 407 TYR 0.005 0.001 TYR B 330 ARG 0.004 0.001 ARG A 76 ********************** 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 131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 TYR cc_start: 0.7555 (t80) cc_final: 0.7058 (t80) REVERT: B 375 TRP cc_start: 0.9273 (p90) cc_final: 0.8893 (p90) REVERT: B 389 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9228 (tptp) REVERT: B 413 HIS cc_start: 0.8772 (m-70) cc_final: 0.8386 (m-70) REVERT: B 418 GLN cc_start: 0.9059 (tt0) cc_final: 0.8484 (tt0) REVERT: A 80 MET cc_start: 0.9111 (tmm) cc_final: 0.8794 (tmm) REVERT: A 355 ASN cc_start: 0.9352 (t0) cc_final: 0.8728 (t0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0993 time to fit residues: 18.1971 Evaluate side-chains 107 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.114197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084225 restraints weight = 12159.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086761 restraints weight = 8245.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088546 restraints weight = 6282.485| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4397 Z= 0.163 Angle : 0.545 6.398 6060 Z= 0.276 Chirality : 0.040 0.138 762 Planarity : 0.004 0.057 775 Dihedral : 10.451 133.579 900 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.47 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 (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: 2.06 (0.36), residues: 634 helix: 2.64 (0.26), residues: 412 sheet: -1.63 (0.75), residues: 47 loop : -0.95 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.004 0.001 HIS A 413 PHE 0.019 0.001 PHE A 407 TYR 0.020 0.001 TYR A 396 ARG 0.006 0.001 ARG A 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.06 seconds wall clock time: 32 minutes 58.81 seconds (1978.81 seconds total)