Starting phenix.real_space_refine on Thu Jan 16 12:20:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ur3_42480/01_2025/8ur3_42480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ur3_42480/01_2025/8ur3_42480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ur3_42480/01_2025/8ur3_42480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ur3_42480/01_2025/8ur3_42480.map" model { file = "/net/cci-nas-00/data/ceres_data/8ur3_42480/01_2025/8ur3_42480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ur3_42480/01_2025/8ur3_42480.cif" } resolution = 2.61 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= 0.021 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 44 5.16 5 C 5982 2.51 5 N 1544 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9376 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ARG A 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG A 78 " occ=0.86 residue: pdb=" N GLY A 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY A 79 " occ=0.82 residue: pdb=" N GLY A 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY A 80 " occ=0.83 residue: pdb=" N ARG A 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG A 81 " occ=0.62 residue: pdb=" N ARG B 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG B 78 " occ=0.86 residue: pdb=" N GLY B 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY B 79 " occ=0.82 residue: pdb=" N GLY B 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY B 80 " occ=0.83 residue: pdb=" N ARG B 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG B 81 " occ=0.62 Time building chain proxies: 5.99, per 1000 atoms: 0.64 Number of scatterers: 9376 At special positions: 0 Unit cell: (101.268, 115.884, 82.476, 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 44 16.00 O 1806 8.00 N 1544 7.00 C 5982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 42.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.536A pdb=" N ALA A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.519A pdb=" N ASN A 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.991A pdb=" N ASP A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.596A pdb=" N PHE A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.571A pdb=" N ILE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE A 209 " --> pdb=" O VAL A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.533A pdb=" N HIS A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.670A pdb=" N GLY A 330 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.643A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.584A pdb=" N SER A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.682A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.536A pdb=" N ALA B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.521A pdb=" N ASN B 22 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.988A pdb=" N ASP B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.593A pdb=" N PHE B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.571A pdb=" N ILE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.525A pdb=" N HIS B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.663A pdb=" N GLY B 330 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.640A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 523 removed outlier: 3.584A pdb=" N SER B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.681A pdb=" N ASN B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 562 through 576 Processing helix chain 'B' and resid 579 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.273A pdb=" N ILE A 52 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU A 245 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE A 54 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 25 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU A 55 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 27 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 289 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 286 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE A 494 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 288 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.384A pdb=" N MET A 389 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 413 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL A 346 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257 removed outlier: 6.032A pdb=" N VAL A 250 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP A 270 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 252 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 266 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP A 256 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 264 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.268A pdb=" N ILE B 52 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU B 245 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 54 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 25 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 55 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 27 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR B 289 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA B 492 " --> pdb=" O ASP B 284 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 286 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE B 494 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 288 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133 removed outlier: 4.385A pdb=" N MET B 389 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 413 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL B 346 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.037A pdb=" N VAL B 250 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 270 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 252 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 266 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP B 256 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA B 264 " --> pdb=" O ASP B 256 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3033 1.34 - 1.46: 1785 1.46 - 1.57: 4702 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9592 Sorted by residual: bond pdb=" C ILE A 581 " pdb=" O ILE A 581 " ideal model delta sigma weight residual 1.237 1.225 0.013 1.17e-02 7.31e+03 1.15e+00 bond pdb=" N ILE A 461 " pdb=" CA ILE A 461 " ideal model delta sigma weight residual 1.458 1.450 0.008 7.70e-03 1.69e+04 1.02e+00 bond pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CA ILE A 461 " pdb=" C ILE A 461 " ideal model delta sigma weight residual 1.528 1.536 -0.008 8.50e-03 1.38e+04 9.33e-01 bond pdb=" CB GLU B 110 " pdb=" CG GLU B 110 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.23e-01 ... (remaining 9587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 12595 1.22 - 2.45: 316 2.45 - 3.67: 65 3.67 - 4.90: 10 4.90 - 6.12: 12 Bond angle restraints: 12998 Sorted by residual: angle pdb=" C HIS A 588 " pdb=" N LYS A 589 " pdb=" CA LYS A 589 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.14e+00 angle pdb=" C HIS B 588 " pdb=" N LYS B 589 " pdb=" CA LYS B 589 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.07e+00 angle pdb=" C GLN A 396 " pdb=" N GLN A 397 " pdb=" CA GLN A 397 " ideal model delta sigma weight residual 121.70 126.19 -4.49 1.80e+00 3.09e-01 6.21e+00 angle pdb=" C GLN B 396 " pdb=" N GLN B 397 " pdb=" CA GLN B 397 " ideal model delta sigma weight residual 121.70 126.16 -4.46 1.80e+00 3.09e-01 6.14e+00 angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 113.47 111.16 2.31 1.01e+00 9.80e-01 5.25e+00 ... (remaining 12993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 5074 14.66 - 29.33: 498 29.33 - 43.99: 134 43.99 - 58.66: 24 58.66 - 73.32: 16 Dihedral angle restraints: 5746 sinusoidal: 2336 harmonic: 3410 Sorted by residual: dihedral pdb=" CA VAL B 483 " pdb=" C VAL B 483 " pdb=" N VAL B 484 " pdb=" CA VAL B 484 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA VAL A 483 " pdb=" C VAL A 483 " pdb=" N VAL A 484 " pdb=" CA VAL A 484 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CG ARG B 540 " pdb=" CD ARG B 540 " pdb=" NE ARG B 540 " pdb=" CZ ARG B 540 " ideal model delta sinusoidal sigma weight residual -90.00 -130.89 40.89 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 5743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 771 0.030 - 0.059: 406 0.059 - 0.089: 157 0.089 - 0.119: 60 0.119 - 0.148: 32 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE B 278 " pdb=" CA ILE B 278 " pdb=" CG1 ILE B 278 " pdb=" CG2 ILE B 278 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE A 529 " pdb=" N ILE A 529 " pdb=" C ILE A 529 " pdb=" CB ILE A 529 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1423 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 190 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO B 191 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 190 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 191 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 231 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.44e+00 pdb=" N PRO A 232 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.017 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2281 2.78 - 3.31: 8750 3.31 - 3.84: 16605 3.84 - 4.37: 20500 4.37 - 4.90: 33708 Nonbonded interactions: 81844 Sorted by model distance: nonbonded pdb=" O THR A 185 " pdb=" OH TYR A 412 " model vdw 2.253 3.040 nonbonded pdb=" O THR B 185 " pdb=" OH TYR B 412 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 431 " pdb=" OD1 ASN A 433 " model vdw 2.265 3.040 nonbonded pdb=" OG SER B 431 " pdb=" OD1 ASN B 433 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 301 " pdb=" OG1 THR A 304 " model vdw 2.273 3.040 ... (remaining 81839 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: 0.04 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=0.62 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: 4.680 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 0.031 9592 Z= 0.215 Angle : 0.513 6.122 12998 Z= 0.274 Chirality : 0.045 0.148 1426 Planarity : 0.003 0.030 1668 Dihedral : 13.471 73.321 3542 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.63 (0.23), residues: 1150 helix: -0.69 (0.23), residues: 388 sheet: 0.20 (0.47), residues: 142 loop : -0.26 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 344 HIS 0.003 0.001 HIS B 208 PHE 0.009 0.001 PHE A 11 TYR 0.008 0.001 TYR A 464 ARG 0.001 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8543 (pm20) cc_final: 0.8293 (pm20) REVERT: A 19 ASN cc_start: 0.8463 (t0) cc_final: 0.8248 (t0) REVERT: A 132 GLN cc_start: 0.8494 (mp10) cc_final: 0.7930 (mp10) REVERT: A 233 MET cc_start: 0.9133 (mtm) cc_final: 0.8891 (mtm) REVERT: A 261 GLN cc_start: 0.8713 (pt0) cc_final: 0.8181 (pm20) REVERT: A 401 ASP cc_start: 0.8650 (m-30) cc_final: 0.8080 (t0) REVERT: A 564 MET cc_start: 0.7545 (mmp) cc_final: 0.6731 (tpt) REVERT: B 18 GLU cc_start: 0.8538 (pm20) cc_final: 0.8296 (pm20) REVERT: B 19 ASN cc_start: 0.8466 (t0) cc_final: 0.8250 (t0) REVERT: B 132 GLN cc_start: 0.8488 (mp10) cc_final: 0.7931 (mp10) REVERT: B 233 MET cc_start: 0.9148 (mtm) cc_final: 0.8909 (mtm) REVERT: B 261 GLN cc_start: 0.8710 (pt0) cc_final: 0.8186 (pm20) REVERT: B 564 MET cc_start: 0.7572 (mmp) cc_final: 0.6684 (tpt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.6227 time to fit residues: 195.8685 Evaluate side-chains 67 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 HIS B 442 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063602 restraints weight = 20955.046| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.74 r_work: 0.2858 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9592 Z= 0.180 Angle : 0.478 4.970 12998 Z= 0.258 Chirality : 0.044 0.158 1426 Planarity : 0.003 0.027 1668 Dihedral : 4.018 15.329 1252 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.96 % Allowed : 6.35 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.21 (0.25), residues: 1150 helix: 0.63 (0.26), residues: 394 sheet: -0.06 (0.46), residues: 136 loop : -0.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 316 HIS 0.001 0.000 HIS B 208 PHE 0.012 0.001 PHE A 506 TYR 0.014 0.001 TYR A 112 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8640 (pm20) cc_final: 0.8439 (pm20) REVERT: A 132 GLN cc_start: 0.8538 (mp10) cc_final: 0.7855 (mp10) REVERT: A 159 GLU cc_start: 0.8913 (mp0) cc_final: 0.8652 (pm20) REVERT: A 261 GLN cc_start: 0.8661 (pt0) cc_final: 0.8192 (pm20) REVERT: A 401 ASP cc_start: 0.8651 (m-30) cc_final: 0.8022 (t0) REVERT: A 564 MET cc_start: 0.7264 (mmp) cc_final: 0.6483 (tpt) REVERT: B 18 GLU cc_start: 0.8635 (pm20) cc_final: 0.8435 (pm20) REVERT: B 132 GLN cc_start: 0.8557 (mp10) cc_final: 0.7877 (mp10) REVERT: B 159 GLU cc_start: 0.8896 (mp0) cc_final: 0.8639 (pm20) REVERT: B 261 GLN cc_start: 0.8658 (pt0) cc_final: 0.8201 (pm20) REVERT: B 401 ASP cc_start: 0.8652 (m-30) cc_final: 0.8036 (t0) REVERT: B 564 MET cc_start: 0.7281 (mmp) cc_final: 0.6547 (tpt) REVERT: B 574 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8517 (pptt) REVERT: B 586 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8597 (mttm) outliers start: 10 outliers final: 2 residues processed: 77 average time/residue: 1.4746 time to fit residues: 121.3664 Evaluate side-chains 66 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 586 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.0970 chunk 1 optimal weight: 0.0870 overall best weight: 1.0558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061188 restraints weight = 21366.747| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.76 r_work: 0.2817 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9592 Z= 0.215 Angle : 0.463 4.913 12998 Z= 0.249 Chirality : 0.043 0.152 1426 Planarity : 0.003 0.024 1668 Dihedral : 3.936 15.063 1252 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.48 % Allowed : 9.81 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.65 (0.25), residues: 1150 helix: 1.21 (0.27), residues: 394 sheet: -0.20 (0.45), residues: 138 loop : 0.19 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.003 0.001 HIS A 442 PHE 0.016 0.001 PHE A 506 TYR 0.011 0.001 TYR A 112 ARG 0.004 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8551 (mp10) cc_final: 0.7854 (mp10) REVERT: A 564 MET cc_start: 0.7300 (mmp) cc_final: 0.6422 (tmm) REVERT: B 132 GLN cc_start: 0.8551 (mp10) cc_final: 0.7862 (mp10) REVERT: B 564 MET cc_start: 0.7341 (mmp) cc_final: 0.6676 (tpt) outliers start: 5 outliers final: 0 residues processed: 67 average time/residue: 1.3271 time to fit residues: 95.9721 Evaluate side-chains 60 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 0.0370 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059032 restraints weight = 21022.904| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.66 r_work: 0.2768 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9592 Z= 0.367 Angle : 0.520 5.056 12998 Z= 0.281 Chirality : 0.046 0.147 1426 Planarity : 0.003 0.027 1668 Dihedral : 4.199 15.460 1252 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 9.81 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.69 (0.25), residues: 1150 helix: 1.35 (0.27), residues: 394 sheet: -0.42 (0.44), residues: 138 loop : 0.19 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.004 0.001 HIS A 442 PHE 0.024 0.001 PHE A 506 TYR 0.012 0.001 TYR A 226 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8692 (mp10) cc_final: 0.7886 (mp10) REVERT: A 173 ASP cc_start: 0.9169 (m-30) cc_final: 0.8660 (p0) REVERT: A 198 MET cc_start: 0.9315 (tpt) cc_final: 0.8884 (tpt) REVERT: A 550 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7896 (p0) REVERT: A 564 MET cc_start: 0.7532 (mmp) cc_final: 0.6631 (tmm) REVERT: B 132 GLN cc_start: 0.8693 (mp10) cc_final: 0.7888 (mp10) REVERT: B 173 ASP cc_start: 0.9165 (m-30) cc_final: 0.8664 (p0) REVERT: B 198 MET cc_start: 0.9308 (tpt) cc_final: 0.8865 (tpt) REVERT: B 550 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7916 (p0) REVERT: B 564 MET cc_start: 0.7476 (mmp) cc_final: 0.6748 (tpt) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 1.3338 time to fit residues: 94.8987 Evaluate side-chains 65 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 550 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059739 restraints weight = 20748.524| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.67 r_work: 0.2783 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9592 Z= 0.269 Angle : 0.488 4.982 12998 Z= 0.263 Chirality : 0.044 0.146 1426 Planarity : 0.003 0.027 1668 Dihedral : 4.086 15.875 1252 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.73 % Allowed : 9.71 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.76 (0.25), residues: 1150 helix: 1.48 (0.27), residues: 396 sheet: -0.57 (0.43), residues: 138 loop : 0.24 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 316 HIS 0.003 0.001 HIS A 442 PHE 0.016 0.001 PHE A 506 TYR 0.010 0.001 TYR A 112 ARG 0.002 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8541 (mp10) cc_final: 0.7670 (mp10) REVERT: A 173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8497 (p0) REVERT: A 198 MET cc_start: 0.9148 (tpt) cc_final: 0.8655 (tpt) REVERT: A 400 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8643 (mmmm) REVERT: A 564 MET cc_start: 0.7437 (mmp) cc_final: 0.6530 (tmm) REVERT: B 132 GLN cc_start: 0.8540 (mp10) cc_final: 0.7670 (mp10) REVERT: B 173 ASP cc_start: 0.8971 (m-30) cc_final: 0.8500 (p0) REVERT: B 198 MET cc_start: 0.9145 (tpt) cc_final: 0.8640 (tpt) REVERT: B 400 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8644 (mmmm) REVERT: B 539 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8328 (mm) REVERT: B 560 LYS cc_start: 0.8815 (tmmt) cc_final: 0.8607 (ttpp) REVERT: B 564 MET cc_start: 0.7388 (mmp) cc_final: 0.6716 (tpt) outliers start: 18 outliers final: 7 residues processed: 71 average time/residue: 1.4681 time to fit residues: 111.7573 Evaluate side-chains 70 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060527 restraints weight = 20810.924| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.69 r_work: 0.2808 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9592 Z= 0.192 Angle : 0.460 5.440 12998 Z= 0.247 Chirality : 0.043 0.144 1426 Planarity : 0.003 0.027 1668 Dihedral : 3.920 15.597 1252 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.83 % Allowed : 10.19 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.86 (0.25), residues: 1150 helix: 1.59 (0.27), residues: 396 sheet: -0.58 (0.43), residues: 138 loop : 0.29 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 442 PHE 0.013 0.001 PHE B 506 TYR 0.010 0.001 TYR B 112 ARG 0.002 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7949 (mtt90) REVERT: A 132 GLN cc_start: 0.8554 (mp10) cc_final: 0.7768 (mp10) REVERT: A 173 ASP cc_start: 0.8954 (m-30) cc_final: 0.8564 (p0) REVERT: A 198 MET cc_start: 0.9143 (tpt) cc_final: 0.8727 (tpt) REVERT: A 506 PHE cc_start: 0.9088 (t80) cc_final: 0.8840 (t80) REVERT: A 564 MET cc_start: 0.7344 (mmp) cc_final: 0.6434 (tmm) REVERT: B 81 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7915 (mtt90) REVERT: B 132 GLN cc_start: 0.8558 (mp10) cc_final: 0.7766 (mp10) REVERT: B 173 ASP cc_start: 0.8961 (m-30) cc_final: 0.8569 (p0) REVERT: B 198 MET cc_start: 0.9152 (tpt) cc_final: 0.8737 (tpt) REVERT: B 506 PHE cc_start: 0.9086 (t80) cc_final: 0.8840 (t80) REVERT: B 539 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 564 MET cc_start: 0.7365 (mmp) cc_final: 0.6492 (tmm) outliers start: 19 outliers final: 7 residues processed: 74 average time/residue: 1.4202 time to fit residues: 112.7804 Evaluate side-chains 69 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 550 ASN ** 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 = 0.3244 r_free = 0.3244 target = 0.073668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060303 restraints weight = 21088.926| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.64 r_work: 0.2797 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9592 Z= 0.246 Angle : 0.492 6.056 12998 Z= 0.265 Chirality : 0.044 0.141 1426 Planarity : 0.003 0.032 1668 Dihedral : 4.010 15.231 1252 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.92 % Allowed : 10.00 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.87 (0.25), residues: 1150 helix: 1.55 (0.27), residues: 398 sheet: -0.56 (0.43), residues: 138 loop : 0.32 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 316 HIS 0.003 0.001 HIS A 442 PHE 0.013 0.001 PHE B 506 TYR 0.011 0.001 TYR A 226 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8693 (mp10) cc_final: 0.7945 (mp10) REVERT: A 173 ASP cc_start: 0.9143 (m-30) cc_final: 0.8624 (p0) REVERT: A 198 MET cc_start: 0.9270 (tpt) cc_final: 0.8844 (tpt) REVERT: A 564 MET cc_start: 0.7489 (mmp) cc_final: 0.6451 (tmm) REVERT: B 132 GLN cc_start: 0.8690 (mp10) cc_final: 0.7935 (mp10) REVERT: B 173 ASP cc_start: 0.9153 (m-30) cc_final: 0.8631 (p0) REVERT: B 198 MET cc_start: 0.9280 (tpt) cc_final: 0.8853 (tpt) REVERT: B 564 MET cc_start: 0.7509 (mmp) cc_final: 0.6800 (tpt) outliers start: 20 outliers final: 9 residues processed: 69 average time/residue: 1.2436 time to fit residues: 92.9966 Evaluate side-chains 69 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 508 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061849 restraints weight = 21492.189| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.79 r_work: 0.2825 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9592 Z= 0.156 Angle : 0.459 6.528 12998 Z= 0.247 Chirality : 0.043 0.141 1426 Planarity : 0.003 0.031 1668 Dihedral : 3.858 14.978 1252 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.25 % Allowed : 11.15 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.94 (0.25), residues: 1150 helix: 1.63 (0.27), residues: 396 sheet: -0.51 (0.43), residues: 138 loop : 0.36 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS B 588 PHE 0.010 0.001 PHE B 506 TYR 0.011 0.001 TYR B 112 ARG 0.002 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8574 (mp10) cc_final: 0.7865 (mp10) REVERT: A 173 ASP cc_start: 0.8962 (m-30) cc_final: 0.8583 (p0) REVERT: A 198 MET cc_start: 0.9146 (tpt) cc_final: 0.8716 (tpt) REVERT: A 506 PHE cc_start: 0.9059 (t80) cc_final: 0.8805 (t80) REVERT: A 564 MET cc_start: 0.7381 (mmp) cc_final: 0.6409 (tmm) REVERT: B 132 GLN cc_start: 0.8584 (mp10) cc_final: 0.7874 (mp10) REVERT: B 173 ASP cc_start: 0.8953 (m-30) cc_final: 0.8577 (p0) REVERT: B 198 MET cc_start: 0.9167 (tpt) cc_final: 0.8767 (tpt) REVERT: B 506 PHE cc_start: 0.9070 (t80) cc_final: 0.8817 (t80) REVERT: B 543 MET cc_start: 0.8431 (mtm) cc_final: 0.8006 (ptp) REVERT: B 564 MET cc_start: 0.7338 (mmp) cc_final: 0.6376 (tmm) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 1.2327 time to fit residues: 89.5253 Evaluate side-chains 66 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 508 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 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 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061353 restraints weight = 21047.202| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.73 r_work: 0.2819 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9592 Z= 0.181 Angle : 0.467 6.815 12998 Z= 0.251 Chirality : 0.043 0.139 1426 Planarity : 0.003 0.032 1668 Dihedral : 3.858 14.792 1252 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.67 % Allowed : 11.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.96 (0.25), residues: 1150 helix: 1.62 (0.27), residues: 396 sheet: -0.46 (0.43), residues: 138 loop : 0.38 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 442 PHE 0.010 0.001 PHE B 506 TYR 0.010 0.001 TYR A 112 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8537 (mp10) cc_final: 0.7801 (mp10) REVERT: A 173 ASP cc_start: 0.8968 (m-30) cc_final: 0.8584 (p0) REVERT: A 198 MET cc_start: 0.9159 (tpt) cc_final: 0.8718 (tpt) REVERT: A 506 PHE cc_start: 0.9063 (t80) cc_final: 0.8799 (t80) REVERT: A 543 MET cc_start: 0.8444 (mtm) cc_final: 0.8017 (ptp) REVERT: A 564 MET cc_start: 0.7415 (mmp) cc_final: 0.6414 (tmm) REVERT: B 132 GLN cc_start: 0.8533 (mp10) cc_final: 0.7791 (mp10) REVERT: B 173 ASP cc_start: 0.8978 (m-30) cc_final: 0.8584 (p0) REVERT: B 198 MET cc_start: 0.9167 (tpt) cc_final: 0.8728 (tpt) REVERT: B 506 PHE cc_start: 0.9053 (t80) cc_final: 0.8789 (t80) REVERT: B 543 MET cc_start: 0.8427 (mtm) cc_final: 0.8002 (ptp) REVERT: B 564 MET cc_start: 0.7391 (mmp) cc_final: 0.6410 (tmm) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 1.3060 time to fit residues: 89.3266 Evaluate side-chains 67 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061594 restraints weight = 21287.713| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.76 r_work: 0.2819 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9592 Z= 0.177 Angle : 0.468 6.267 12998 Z= 0.250 Chirality : 0.043 0.139 1426 Planarity : 0.003 0.032 1668 Dihedral : 3.842 14.651 1252 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.58 % Allowed : 11.73 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.99 (0.25), residues: 1150 helix: 1.65 (0.27), residues: 396 sheet: -0.43 (0.43), residues: 138 loop : 0.38 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 442 PHE 0.010 0.001 PHE B 506 TYR 0.010 0.001 TYR B 112 ARG 0.003 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8556 (mp10) cc_final: 0.7826 (mp10) REVERT: A 173 ASP cc_start: 0.8963 (m-30) cc_final: 0.8604 (p0) REVERT: A 198 MET cc_start: 0.9159 (tpt) cc_final: 0.8730 (tpt) REVERT: A 506 PHE cc_start: 0.9061 (t80) cc_final: 0.8801 (t80) REVERT: A 543 MET cc_start: 0.8512 (mtm) cc_final: 0.8101 (ptp) REVERT: A 564 MET cc_start: 0.7401 (mmp) cc_final: 0.6405 (tmm) REVERT: B 132 GLN cc_start: 0.8567 (mp10) cc_final: 0.7838 (mp10) REVERT: B 173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8605 (p0) REVERT: B 198 MET cc_start: 0.9177 (tpt) cc_final: 0.8752 (tpt) REVERT: B 506 PHE cc_start: 0.9061 (t80) cc_final: 0.8803 (t80) REVERT: B 543 MET cc_start: 0.8463 (mtm) cc_final: 0.8068 (ptp) REVERT: B 564 MET cc_start: 0.7396 (mmp) cc_final: 0.6422 (tmm) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 1.3289 time to fit residues: 90.6899 Evaluate side-chains 68 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 111 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062672 restraints weight = 21161.054| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.72 r_work: 0.2846 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9592 Z= 0.140 Angle : 0.449 7.088 12998 Z= 0.241 Chirality : 0.042 0.138 1426 Planarity : 0.003 0.030 1668 Dihedral : 3.730 14.327 1252 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.58 % Allowed : 11.92 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 1.04 (0.26), residues: 1150 helix: 1.68 (0.27), residues: 396 sheet: -0.38 (0.43), residues: 138 loop : 0.41 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.000 HIS B 588 PHE 0.008 0.001 PHE B 506 TYR 0.011 0.001 TYR B 112 ARG 0.002 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.45 seconds wall clock time: 93 minutes 34.94 seconds (5614.94 seconds total)