Starting phenix.real_space_refine on Sat Aug 3 07:51:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/08_2024/8wx3_37899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/08_2024/8wx3_37899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/08_2024/8wx3_37899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/08_2024/8wx3_37899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/08_2024/8wx3_37899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/08_2024/8wx3_37899.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4954 2.51 5 N 1226 2.21 5 O 1278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7498 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3749 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain breaks: 2 Chain: "B" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3749 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain breaks: 2 Time building chain proxies: 4.63, per 1000 atoms: 0.62 Number of scatterers: 7498 At special positions: 0 Unit cell: (83.415, 120.765, 83.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1278 8.00 N 1226 7.00 C 4954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 77.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 33 through 56 removed outlier: 3.601A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.627A pdb=" N SER A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 103 through 118 removed outlier: 3.695A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 125 through 133 removed outlier: 4.158A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.611A pdb=" N THR A 157 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.681A pdb=" N ALA A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 187 through 212 removed outlier: 3.518A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 221 through 244 removed outlier: 3.634A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 328 through 347 removed outlier: 3.892A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.825A pdb=" N THR A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.656A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 400 through 428 removed outlier: 3.633A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 480 removed outlier: 4.809A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 510 Processing helix chain 'A' and resid 531 through 563 removed outlier: 3.880A pdb=" N HIS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.802A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.514A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 125 through 133 removed outlier: 4.323A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 182 removed outlier: 3.972A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 3.809A pdb=" N GLN B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 removed outlier: 3.549A pdb=" N ARG B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 187 through 212 removed outlier: 3.557A pdb=" N TRP B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.612A pdb=" N GLY B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.684A pdb=" N LEU B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 347 Proline residue: B 330 - end of helix removed outlier: 3.698A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.280A pdb=" N LEU B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.571A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 400 through 430 removed outlier: 3.585A pdb=" N ASN B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.679A pdb=" N ILE B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 471 " --> pdb=" O PHE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 511 removed outlier: 3.593A pdb=" N SER B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 559 removed outlier: 3.539A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 556 " --> pdb=" O ILE B 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AA2, first strand: chain 'B' and resid 435 through 438 510 hydrogen bonds defined for protein. 1509 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: 2.14 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2301 1.35 - 1.47: 1959 1.47 - 1.59: 3366 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 7686 Sorted by residual: bond pdb=" C SER A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.335 1.367 -0.031 1.36e-02 5.41e+03 5.24e+00 bond pdb=" C SER B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" CA ALA A 65 " pdb=" C ALA A 65 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.61e+00 bond pdb=" N ILE A 354 " pdb=" CA ILE A 354 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" CA ALA B 65 " pdb=" C ALA B 65 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.26e-02 6.30e+03 1.07e+00 ... (remaining 7681 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.12: 173 106.12 - 113.10: 4155 113.10 - 120.08: 2881 120.08 - 127.06: 3156 127.06 - 134.05: 91 Bond angle restraints: 10456 Sorted by residual: angle pdb=" N ILE A 263 " pdb=" CA ILE A 263 " pdb=" C ILE A 263 " ideal model delta sigma weight residual 113.47 108.96 4.51 1.01e+00 9.80e-01 1.99e+01 angle pdb=" N ILE B 357 " pdb=" CA ILE B 357 " pdb=" C ILE B 357 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N VAL B 246 " pdb=" CA VAL B 246 " pdb=" C VAL B 246 " ideal model delta sigma weight residual 113.47 109.35 4.12 1.01e+00 9.80e-01 1.67e+01 angle pdb=" N ILE B 354 " pdb=" CA ILE B 354 " pdb=" C ILE B 354 " ideal model delta sigma weight residual 106.21 109.92 -3.71 1.07e+00 8.73e-01 1.20e+01 angle pdb=" C ALA A 65 " pdb=" CA ALA A 65 " pdb=" CB ALA A 65 " ideal model delta sigma weight residual 110.17 116.74 -6.57 1.97e+00 2.58e-01 1.11e+01 ... (remaining 10451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4081 17.45 - 34.89: 334 34.89 - 52.34: 35 52.34 - 69.79: 5 69.79 - 87.23: 7 Dihedral angle restraints: 4462 sinusoidal: 1670 harmonic: 2792 Sorted by residual: dihedral pdb=" CA GLY A 83 " pdb=" C GLY A 83 " pdb=" N LEU A 84 " pdb=" CA LEU A 84 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" SG CYS B 133 " pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" CA CYS B 153 " ideal model delta sinusoidal sigma weight residual -73.00 -6.70 -66.30 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" CA ALA B 65 " pdb=" C ALA B 65 " pdb=" N PRO B 66 " pdb=" CA PRO B 66 " ideal model delta harmonic sigma weight residual 180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 675 0.028 - 0.056: 387 0.056 - 0.084: 99 0.084 - 0.111: 50 0.111 - 0.139: 13 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA VAL A 220 " pdb=" N VAL A 220 " pdb=" C VAL A 220 " pdb=" CB VAL A 220 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE B 351 " pdb=" N ILE B 351 " pdb=" C ILE B 351 " pdb=" CB ILE B 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL A 442 " pdb=" N VAL A 442 " pdb=" C VAL A 442 " pdb=" CB VAL A 442 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1221 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 65 " 0.048 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO B 66 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 65 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 66 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 174 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" CG ASN A 174 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 174 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 174 " -0.008 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 611 2.74 - 3.28: 7941 3.28 - 3.82: 12732 3.82 - 4.36: 14995 4.36 - 4.90: 25762 Nonbonded interactions: 62041 Sorted by model distance: nonbonded pdb=" OE1 GLN A 337 " pdb=" OH TYR A 535 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG B 33 " pdb=" OD1 ASP B 185 " model vdw 2.263 3.120 nonbonded pdb=" OE1 GLN B 345 " pdb=" NE2 GLN B 454 " model vdw 2.307 3.120 nonbonded pdb=" O LEU B 122 " pdb=" OG1 THR B 128 " model vdw 2.313 3.040 nonbonded pdb=" OD2 ASP A 259 " pdb=" NZ LYS A 311 " model vdw 2.327 3.120 ... (remaining 62036 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' selection = chain 'B' } 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 individual isotropic 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.310 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 : 0.003 0.044 7686 Z= 0.205 Angle : 0.700 7.328 10456 Z= 0.441 Chirality : 0.039 0.139 1224 Planarity : 0.004 0.070 1290 Dihedral : 12.635 87.232 2658 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.33 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 962 helix: 1.13 (0.21), residues: 662 sheet: None (None), residues: 0 loop : -1.42 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 69 HIS 0.001 0.000 HIS A 521 PHE 0.012 0.001 PHE A 61 TYR 0.016 0.001 TYR A 335 ARG 0.010 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.793 Fit side-chains REVERT: A 104 ARG cc_start: 0.6756 (mtp85) cc_final: 0.6415 (mtp85) REVERT: A 113 TYR cc_start: 0.8010 (t80) cc_final: 0.7802 (t80) REVERT: A 129 ARG cc_start: 0.6549 (ttm110) cc_final: 0.6346 (ttm110) REVERT: A 189 GLU cc_start: 0.6114 (pm20) cc_final: 0.5697 (tm-30) REVERT: A 250 LYS cc_start: 0.7710 (ptmm) cc_final: 0.7021 (mttt) REVERT: A 339 GLN cc_start: 0.7591 (mt0) cc_final: 0.7264 (mt0) REVERT: A 353 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6639 (mm-30) REVERT: A 482 LYS cc_start: 0.8005 (mppt) cc_final: 0.7395 (mmtp) REVERT: A 484 MET cc_start: 0.6920 (mtm) cc_final: 0.6475 (mtp) REVERT: B 34 ARG cc_start: 0.7112 (ttm170) cc_final: 0.6853 (ttp-170) REVERT: B 112 LEU cc_start: 0.7687 (mt) cc_final: 0.7439 (mp) REVERT: B 129 ARG cc_start: 0.6251 (ttm110) cc_final: 0.5963 (ttm110) REVERT: B 242 CYS cc_start: 0.7997 (m) cc_final: 0.7194 (t) REVERT: B 250 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7284 (mttt) REVERT: B 372 PHE cc_start: 0.5441 (t80) cc_final: 0.4774 (t80) REVERT: B 386 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6938 (mmtp) REVERT: B 403 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7258 (mmtm) REVERT: B 409 MET cc_start: 0.8298 (mtp) cc_final: 0.8022 (mtt) REVERT: B 482 LYS cc_start: 0.7791 (mppt) cc_final: 0.7220 (mmtp) REVERT: B 501 PHE cc_start: 0.7032 (m-80) cc_final: 0.6785 (m-80) REVERT: B 556 LYS cc_start: 0.7294 (mttt) cc_final: 0.6723 (mtpt) REVERT: B 558 ASP cc_start: 0.7445 (m-30) cc_final: 0.7157 (m-30) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.9909 time to fit residues: 186.9140 Evaluate side-chains 127 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 24 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 454 GLN A 485 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7686 Z= 0.178 Angle : 0.571 7.768 10456 Z= 0.291 Chirality : 0.039 0.181 1224 Planarity : 0.005 0.069 1290 Dihedral : 3.880 19.788 1038 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.57 % Rotamer: Outliers : 2.05 % Allowed : 9.34 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.11 (0.28), residues: 962 helix: 1.64 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.003 0.001 HIS A 559 PHE 0.017 0.001 PHE A 67 TYR 0.021 0.001 TYR A 113 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.852 Fit side-chains REVERT: A 104 ARG cc_start: 0.6565 (mtp85) cc_final: 0.6212 (mtp85) REVERT: A 129 ARG cc_start: 0.6657 (ttm110) cc_final: 0.6321 (ttm110) REVERT: A 189 GLU cc_start: 0.5868 (pm20) cc_final: 0.5519 (tm-30) REVERT: A 250 LYS cc_start: 0.7872 (ptmm) cc_final: 0.7200 (mttt) REVERT: A 339 GLN cc_start: 0.7552 (mt0) cc_final: 0.7312 (mt0) REVERT: A 353 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6619 (mm-30) REVERT: A 482 LYS cc_start: 0.8008 (mppt) cc_final: 0.7268 (mmtp) REVERT: A 484 MET cc_start: 0.6581 (mtm) cc_final: 0.6112 (mtp) REVERT: B 84 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7689 (mt) REVERT: B 129 ARG cc_start: 0.6369 (ttm110) cc_final: 0.6094 (ttm110) REVERT: B 186 ARG cc_start: 0.7787 (mpp80) cc_final: 0.7502 (mtt90) REVERT: B 242 CYS cc_start: 0.7995 (m) cc_final: 0.7187 (t) REVERT: B 250 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7301 (mttt) REVERT: B 386 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6854 (mmtp) REVERT: B 482 LYS cc_start: 0.7834 (mppt) cc_final: 0.7306 (mmtp) outliers start: 16 outliers final: 6 residues processed: 139 average time/residue: 0.8681 time to fit residues: 129.9301 Evaluate side-chains 129 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 435 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7686 Z= 0.184 Angle : 0.545 7.891 10456 Z= 0.277 Chirality : 0.039 0.137 1224 Planarity : 0.004 0.067 1290 Dihedral : 3.848 20.839 1038 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.57 % Rotamer: Outliers : 2.94 % Allowed : 10.23 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 962 helix: 1.75 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.003 0.001 HIS A 563 PHE 0.017 0.001 PHE A 67 TYR 0.022 0.001 TYR A 113 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.726 Fit side-chains REVERT: A 104 ARG cc_start: 0.6549 (mtp85) cc_final: 0.6260 (mtp85) REVERT: A 112 LEU cc_start: 0.7475 (mt) cc_final: 0.7257 (mp) REVERT: A 129 ARG cc_start: 0.6674 (ttm110) cc_final: 0.6211 (ttm110) REVERT: A 189 GLU cc_start: 0.5775 (pm20) cc_final: 0.5460 (tm-30) REVERT: A 250 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7212 (mttt) REVERT: A 339 GLN cc_start: 0.7515 (mt0) cc_final: 0.7271 (mt0) REVERT: A 353 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6672 (mm-30) REVERT: A 482 LYS cc_start: 0.7884 (mppt) cc_final: 0.7320 (mmtp) REVERT: A 484 MET cc_start: 0.6629 (mtm) cc_final: 0.6305 (mtp) REVERT: B 82 MET cc_start: 0.7396 (mmt) cc_final: 0.7116 (mmp) REVERT: B 97 ASP cc_start: 0.8056 (m-30) cc_final: 0.7493 (m-30) REVERT: B 242 CYS cc_start: 0.7988 (m) cc_final: 0.7217 (t) REVERT: B 250 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7302 (mttt) REVERT: B 386 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6836 (mmtp) REVERT: B 409 MET cc_start: 0.8066 (mtt) cc_final: 0.7805 (mtm) REVERT: B 459 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7115 (mt) REVERT: B 482 LYS cc_start: 0.7838 (mppt) cc_final: 0.7287 (mmtp) REVERT: B 558 ASP cc_start: 0.7068 (m-30) cc_final: 0.6835 (m-30) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 0.9061 time to fit residues: 138.2144 Evaluate side-chains 136 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 553 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.0060 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7686 Z= 0.177 Angle : 0.536 8.040 10456 Z= 0.271 Chirality : 0.038 0.137 1224 Planarity : 0.004 0.065 1290 Dihedral : 3.829 20.734 1038 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.57 % Rotamer: Outliers : 3.07 % Allowed : 11.76 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.43 (0.28), residues: 962 helix: 1.83 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.002 0.001 HIS A 563 PHE 0.018 0.001 PHE A 67 TYR 0.019 0.001 TYR A 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.807 Fit side-chains REVERT: A 112 LEU cc_start: 0.7493 (mt) cc_final: 0.7233 (mp) REVERT: A 129 ARG cc_start: 0.6642 (ttm110) cc_final: 0.6121 (ttm110) REVERT: A 186 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7148 (mtt180) REVERT: A 189 GLU cc_start: 0.5774 (pm20) cc_final: 0.5443 (tm-30) REVERT: A 250 LYS cc_start: 0.7871 (ptmm) cc_final: 0.7178 (mttt) REVERT: A 339 GLN cc_start: 0.7494 (mt0) cc_final: 0.7234 (mt0) REVERT: A 353 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6741 (mm-30) REVERT: A 482 LYS cc_start: 0.7896 (mppt) cc_final: 0.7278 (mmtp) REVERT: A 484 MET cc_start: 0.6660 (mtm) cc_final: 0.6414 (mtp) REVERT: B 82 MET cc_start: 0.7437 (mmt) cc_final: 0.7151 (mmp) REVERT: B 86 TYR cc_start: 0.7103 (m-80) cc_final: 0.6772 (m-80) REVERT: B 97 ASP cc_start: 0.7979 (m-30) cc_final: 0.7382 (m-30) REVERT: B 242 CYS cc_start: 0.7890 (m) cc_final: 0.7210 (t) REVERT: B 250 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7309 (mttt) REVERT: B 386 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6807 (mmtp) REVERT: B 409 MET cc_start: 0.8128 (mtt) cc_final: 0.7799 (mtm) REVERT: B 459 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6981 (mt) REVERT: B 482 LYS cc_start: 0.7838 (mppt) cc_final: 0.7282 (mmtp) outliers start: 24 outliers final: 15 residues processed: 131 average time/residue: 0.8838 time to fit residues: 124.7567 Evaluate side-chains 134 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 31 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7686 Z= 0.161 Angle : 0.525 8.120 10456 Z= 0.263 Chirality : 0.038 0.136 1224 Planarity : 0.004 0.064 1290 Dihedral : 3.763 20.892 1038 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.12 % Favored : 96.67 % Rotamer: Outliers : 3.45 % Allowed : 12.40 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.61 (0.28), residues: 962 helix: 1.97 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 197 HIS 0.002 0.000 HIS A 563 PHE 0.019 0.001 PHE A 67 TYR 0.015 0.001 TYR B 335 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.839 Fit side-chains REVERT: A 112 LEU cc_start: 0.7553 (mt) cc_final: 0.7269 (mp) REVERT: A 129 ARG cc_start: 0.6634 (ttm110) cc_final: 0.6101 (ttm110) REVERT: A 186 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7157 (mtt180) REVERT: A 189 GLU cc_start: 0.5701 (pm20) cc_final: 0.5406 (OUTLIER) REVERT: A 250 LYS cc_start: 0.7870 (ptmm) cc_final: 0.7184 (mttt) REVERT: A 339 GLN cc_start: 0.7447 (mt0) cc_final: 0.7167 (mt0) REVERT: A 353 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6731 (mm-30) REVERT: A 372 PHE cc_start: 0.7301 (m-10) cc_final: 0.5969 (t80) REVERT: A 409 MET cc_start: 0.8192 (mtt) cc_final: 0.7914 (mtm) REVERT: A 482 LYS cc_start: 0.7897 (mppt) cc_final: 0.7246 (mmtp) REVERT: A 484 MET cc_start: 0.6664 (mtm) cc_final: 0.6405 (mtp) REVERT: B 82 MET cc_start: 0.7487 (mmt) cc_final: 0.7218 (mmp) REVERT: B 86 TYR cc_start: 0.7141 (m-80) cc_final: 0.6774 (m-80) REVERT: B 97 ASP cc_start: 0.7956 (m-30) cc_final: 0.7382 (m-30) REVERT: B 242 CYS cc_start: 0.7947 (m) cc_final: 0.7225 (t) REVERT: B 250 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7320 (mttt) REVERT: B 459 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7024 (mt) REVERT: B 482 LYS cc_start: 0.7837 (mppt) cc_final: 0.7277 (mmtp) REVERT: B 558 ASP cc_start: 0.7143 (m-30) cc_final: 0.6940 (m-30) outliers start: 27 outliers final: 17 residues processed: 138 average time/residue: 0.8240 time to fit residues: 123.1105 Evaluate side-chains 133 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 504 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7686 Z= 0.173 Angle : 0.527 7.363 10456 Z= 0.265 Chirality : 0.038 0.139 1224 Planarity : 0.004 0.063 1290 Dihedral : 3.765 21.078 1038 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.01 % Favored : 96.78 % Rotamer: Outliers : 3.58 % Allowed : 12.66 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.64 (0.28), residues: 962 helix: 2.03 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 563 PHE 0.020 0.001 PHE A 67 TYR 0.013 0.001 TYR B 335 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 0.786 Fit side-chains REVERT: A 129 ARG cc_start: 0.6647 (ttm110) cc_final: 0.6084 (ttm110) REVERT: A 186 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7128 (mtt180) REVERT: A 189 GLU cc_start: 0.5699 (pm20) cc_final: 0.5410 (OUTLIER) REVERT: A 250 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7097 (mttt) REVERT: A 339 GLN cc_start: 0.7430 (mt0) cc_final: 0.7095 (mt0) REVERT: A 353 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6694 (mm-30) REVERT: A 372 PHE cc_start: 0.7154 (m-10) cc_final: 0.5970 (t80) REVERT: A 482 LYS cc_start: 0.7844 (mppt) cc_final: 0.7216 (mmtp) REVERT: A 484 MET cc_start: 0.6717 (mtm) cc_final: 0.6514 (mtp) REVERT: B 82 MET cc_start: 0.7504 (mmt) cc_final: 0.7223 (mmp) REVERT: B 86 TYR cc_start: 0.7171 (m-80) cc_final: 0.6676 (m-80) REVERT: B 97 ASP cc_start: 0.7965 (m-30) cc_final: 0.7418 (m-30) REVERT: B 222 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.4799 (t80) REVERT: B 242 CYS cc_start: 0.7951 (m) cc_final: 0.7221 (t) REVERT: B 250 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7448 (mttt) REVERT: B 409 MET cc_start: 0.8080 (mtt) cc_final: 0.7803 (mtm) REVERT: B 459 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7112 (mt) REVERT: B 482 LYS cc_start: 0.7837 (mppt) cc_final: 0.7274 (mmtp) outliers start: 28 outliers final: 18 residues processed: 130 average time/residue: 0.8825 time to fit residues: 123.6431 Evaluate side-chains 130 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 504 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7686 Z= 0.177 Angle : 0.530 8.165 10456 Z= 0.265 Chirality : 0.038 0.140 1224 Planarity : 0.004 0.062 1290 Dihedral : 3.759 21.378 1038 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.33 % Favored : 96.47 % Rotamer: Outliers : 2.94 % Allowed : 13.30 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.63 (0.28), residues: 962 helix: 2.06 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 197 HIS 0.002 0.000 HIS A 563 PHE 0.018 0.001 PHE A 67 TYR 0.013 0.001 TYR B 335 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.743 Fit side-chains REVERT: A 129 ARG cc_start: 0.6631 (ttm110) cc_final: 0.6045 (ttm110) REVERT: A 186 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7131 (mtt180) REVERT: A 189 GLU cc_start: 0.5727 (pm20) cc_final: 0.5424 (OUTLIER) REVERT: A 250 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7112 (mttt) REVERT: A 339 GLN cc_start: 0.7582 (mt0) cc_final: 0.7205 (mt0) REVERT: A 353 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6688 (mm-30) REVERT: A 372 PHE cc_start: 0.7115 (m-10) cc_final: 0.5914 (t80) REVERT: A 409 MET cc_start: 0.8183 (mtt) cc_final: 0.7904 (mtm) REVERT: A 482 LYS cc_start: 0.7836 (mppt) cc_final: 0.7216 (mmtp) REVERT: B 86 TYR cc_start: 0.7349 (m-80) cc_final: 0.6986 (m-80) REVERT: B 97 ASP cc_start: 0.7960 (m-30) cc_final: 0.7413 (m-30) REVERT: B 222 PHE cc_start: 0.5417 (OUTLIER) cc_final: 0.4702 (t80) REVERT: B 242 CYS cc_start: 0.7954 (m) cc_final: 0.7215 (t) REVERT: B 250 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7447 (mttt) REVERT: B 459 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7041 (mt) REVERT: B 482 LYS cc_start: 0.7783 (mppt) cc_final: 0.7236 (mmtp) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.9144 time to fit residues: 121.7931 Evaluate side-chains 125 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7686 Z= 0.189 Angle : 0.537 7.593 10456 Z= 0.269 Chirality : 0.039 0.140 1224 Planarity : 0.004 0.062 1290 Dihedral : 3.789 21.669 1038 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.57 % Rotamer: Outliers : 2.69 % Allowed : 13.81 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.62 (0.28), residues: 962 helix: 2.04 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 517 HIS 0.002 0.001 HIS A 563 PHE 0.017 0.001 PHE A 67 TYR 0.015 0.001 TYR A 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.819 Fit side-chains REVERT: A 55 THR cc_start: 0.7007 (p) cc_final: 0.6789 (p) REVERT: A 129 ARG cc_start: 0.6628 (ttm110) cc_final: 0.6009 (ttm110) REVERT: A 186 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7276 (mtt180) REVERT: A 189 GLU cc_start: 0.5725 (pm20) cc_final: 0.5425 (OUTLIER) REVERT: A 250 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7105 (mttt) REVERT: A 339 GLN cc_start: 0.7600 (mt0) cc_final: 0.7223 (mt0) REVERT: A 353 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6686 (mm-30) REVERT: A 372 PHE cc_start: 0.7201 (m-10) cc_final: 0.6109 (t80) REVERT: A 482 LYS cc_start: 0.7833 (mppt) cc_final: 0.7182 (mmtp) REVERT: B 86 TYR cc_start: 0.7301 (m-80) cc_final: 0.6977 (m-80) REVERT: B 97 ASP cc_start: 0.7954 (m-30) cc_final: 0.7402 (m-30) REVERT: B 186 ARG cc_start: 0.7703 (mpp80) cc_final: 0.7477 (mpp80) REVERT: B 222 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.4745 (t80) REVERT: B 242 CYS cc_start: 0.7959 (m) cc_final: 0.7214 (t) REVERT: B 250 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7428 (mttt) REVERT: B 459 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6982 (mt) REVERT: B 482 LYS cc_start: 0.7800 (mppt) cc_final: 0.7174 (mmtp) outliers start: 21 outliers final: 16 residues processed: 123 average time/residue: 0.9203 time to fit residues: 121.6054 Evaluate side-chains 122 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7686 Z= 0.174 Angle : 0.533 8.342 10456 Z= 0.266 Chirality : 0.039 0.141 1224 Planarity : 0.004 0.061 1290 Dihedral : 3.765 21.508 1038 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.01 % Favored : 96.78 % Rotamer: Outliers : 2.56 % Allowed : 13.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.66 (0.28), residues: 962 helix: 2.07 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 563 PHE 0.016 0.001 PHE A 67 TYR 0.017 0.001 TYR A 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.738 Fit side-chains REVERT: A 129 ARG cc_start: 0.6524 (ttm110) cc_final: 0.6137 (ttm110) REVERT: A 186 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7370 (mtt180) REVERT: A 189 GLU cc_start: 0.5572 (pm20) cc_final: 0.5259 (OUTLIER) REVERT: A 250 LYS cc_start: 0.7835 (ptmm) cc_final: 0.7104 (mttt) REVERT: A 339 GLN cc_start: 0.7565 (mt0) cc_final: 0.7188 (mt0) REVERT: A 353 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6681 (mm-30) REVERT: A 372 PHE cc_start: 0.7178 (m-10) cc_final: 0.6113 (t80) REVERT: A 482 LYS cc_start: 0.7826 (mppt) cc_final: 0.7206 (mmtp) REVERT: A 546 THR cc_start: 0.8086 (p) cc_final: 0.7577 (t) REVERT: B 86 TYR cc_start: 0.7317 (m-80) cc_final: 0.6872 (m-80) REVERT: B 97 ASP cc_start: 0.7960 (m-30) cc_final: 0.7425 (m-30) REVERT: B 186 ARG cc_start: 0.7678 (mpp80) cc_final: 0.7457 (mpp80) REVERT: B 222 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.4881 (t80) REVERT: B 242 CYS cc_start: 0.7957 (m) cc_final: 0.7205 (t) REVERT: B 250 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7428 (mttt) REVERT: B 459 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7025 (mt) REVERT: B 482 LYS cc_start: 0.7796 (mppt) cc_final: 0.7168 (mmtp) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.9270 time to fit residues: 120.2986 Evaluate side-chains 121 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7686 Z= 0.188 Angle : 0.546 8.437 10456 Z= 0.271 Chirality : 0.039 0.142 1224 Planarity : 0.004 0.061 1290 Dihedral : 3.788 21.445 1038 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.33 % Favored : 96.47 % Rotamer: Outliers : 2.81 % Allowed : 14.19 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.64 (0.28), residues: 962 helix: 2.04 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 517 HIS 0.002 0.001 HIS A 563 PHE 0.017 0.001 PHE A 67 TYR 0.018 0.001 TYR A 113 ARG 0.002 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.807 Fit side-chains REVERT: A 129 ARG cc_start: 0.6413 (ttm110) cc_final: 0.5996 (ttm110) REVERT: A 186 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7365 (mtt180) REVERT: A 250 LYS cc_start: 0.7881 (ptmm) cc_final: 0.7190 (mttt) REVERT: A 339 GLN cc_start: 0.7590 (mt0) cc_final: 0.7214 (mt0) REVERT: A 353 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6679 (mm-30) REVERT: A 372 PHE cc_start: 0.7194 (m-10) cc_final: 0.6128 (t80) REVERT: A 482 LYS cc_start: 0.7833 (mppt) cc_final: 0.7177 (mmtp) REVERT: A 546 THR cc_start: 0.8077 (p) cc_final: 0.7579 (t) REVERT: B 86 TYR cc_start: 0.7389 (m-80) cc_final: 0.6964 (m-80) REVERT: B 97 ASP cc_start: 0.7960 (m-30) cc_final: 0.7421 (m-30) REVERT: B 186 ARG cc_start: 0.7651 (mpp80) cc_final: 0.7429 (mpp80) REVERT: B 222 PHE cc_start: 0.5813 (OUTLIER) cc_final: 0.4970 (t80) REVERT: B 242 CYS cc_start: 0.7960 (m) cc_final: 0.7205 (t) REVERT: B 250 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7428 (mttt) REVERT: B 459 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7034 (mt) REVERT: B 482 LYS cc_start: 0.7814 (mppt) cc_final: 0.7146 (mmtp) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.9546 time to fit residues: 123.9034 Evaluate side-chains 121 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100934 restraints weight = 8292.332| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.67 r_work: 0.2904 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7686 Z= 0.183 Angle : 0.549 8.475 10456 Z= 0.271 Chirality : 0.039 0.141 1224 Planarity : 0.004 0.060 1290 Dihedral : 3.778 21.447 1038 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.12 % Favored : 96.67 % Rotamer: Outliers : 2.69 % Allowed : 14.71 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.66 (0.28), residues: 962 helix: 2.04 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 197 HIS 0.002 0.001 HIS A 563 PHE 0.017 0.001 PHE A 67 TYR 0.018 0.001 TYR A 113 ARG 0.002 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.60 seconds wall clock time: 49 minutes 42.81 seconds (2982.81 seconds total)