Starting phenix.real_space_refine on Fri Mar 15 11:57:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/03_2024/6wcc_21606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/03_2024/6wcc_21606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/03_2024/6wcc_21606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/03_2024/6wcc_21606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/03_2024/6wcc_21606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/03_2024/6wcc_21606.pdb" } resolution = 3.24 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cs 5 16.47 5 S 38 5.16 5 C 3758 2.51 5 N 940 2.21 5 O 980 1.98 5 H 5908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5806 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5806 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.60, per 1000 atoms: 0.48 Number of scatterers: 11629 At special positions: 0 Unit cell: (107.712, 66.368, 78.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cs 5 54.66 S 38 16.00 O 980 8.00 N 940 7.00 C 3758 6.00 H 5908 1.00 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 - 3.50 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: 9.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 67 through 103 removed outlier: 4.180A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 333 removed outlier: 3.839A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.624A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.544A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 400 removed outlier: 3.912A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.951A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 67 through 103 removed outlier: 4.180A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 284 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 333 removed outlier: 3.840A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.624A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.544A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 400 removed outlier: 3.912A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.952A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 462 hydrogen bonds defined for protein. 1368 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: 4.38 Time building geometry restraints manager: 10.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5890 1.03 - 1.23: 18 1.23 - 1.42: 2386 1.42 - 1.61: 3394 1.61 - 1.81: 58 Bond restraints: 11746 Sorted by residual: bond pdb=" CG LEU B 470 " pdb=" CD1 LEU B 470 " ideal model delta sigma weight residual 1.521 1.559 -0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" CG PHE A 295 " pdb=" CD2 PHE A 295 " ideal model delta sigma weight residual 1.384 1.360 0.024 2.10e-02 2.27e+03 1.26e+00 bond pdb=" CG LEU A 470 " pdb=" CD1 LEU A 470 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CG PHE B 295 " pdb=" CD2 PHE B 295 " ideal model delta sigma weight residual 1.384 1.361 0.023 2.10e-02 2.27e+03 1.17e+00 bond pdb=" CB GLU B 59 " pdb=" CG GLU B 59 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.96e-01 ... (remaining 11741 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.50: 117 105.50 - 112.62: 13875 112.62 - 119.73: 2791 119.73 - 126.84: 4435 126.84 - 133.96: 78 Bond angle restraints: 21296 Sorted by residual: angle pdb=" CG LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 109.00 98.39 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb="HD21 LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 110.00 100.10 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CG LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD21 LEU A 470 " ideal model delta sigma weight residual 109.00 117.41 -8.41 3.00e+00 1.11e-01 7.85e+00 angle pdb=" CD2 LEU B 470 " pdb=" CG LEU B 470 " pdb=" HG LEU B 470 " ideal model delta sigma weight residual 108.00 100.28 7.72 3.00e+00 1.11e-01 6.63e+00 angle pdb="HD22 LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 110.00 116.89 -6.89 3.00e+00 1.11e-01 5.28e+00 ... (remaining 21291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4918 16.97 - 33.93: 428 33.93 - 50.90: 118 50.90 - 67.86: 58 67.86 - 84.83: 6 Dihedral angle restraints: 5528 sinusoidal: 2936 harmonic: 2592 Sorted by residual: dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASN B 284 " pdb=" CB ASN B 284 " pdb=" CG ASN B 284 " pdb=" OD1 ASN B 284 " ideal model delta sinusoidal sigma weight residual -90.00 -162.72 72.72 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 721 0.027 - 0.053: 128 0.053 - 0.080: 84 0.080 - 0.107: 34 0.107 - 0.134: 11 Chirality restraints: 978 Sorted by residual: chirality pdb=" CG LEU A 470 " pdb=" CB LEU A 470 " pdb=" CD1 LEU A 470 " pdb=" CD2 LEU A 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CG LEU B 470 " pdb=" CB LEU B 470 " pdb=" CD1 LEU B 470 " pdb=" CD2 LEU B 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 975 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 295 " -0.028 2.00e-02 2.50e+03 1.82e-02 9.89e+00 pdb=" CG PHE A 295 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 295 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 295 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 295 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 295 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 295 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 295 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 295 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 295 " 0.022 2.00e-02 2.50e+03 1.78e-02 9.48e+00 pdb=" CG PHE B 295 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 295 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 295 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 295 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 295 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 295 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 295 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 295 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 295 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 295 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 124 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.021 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.60: 12042 2.60 - 3.41: 46823 3.41 - 4.23: 62751 4.23 - 5.04: 110077 5.04 - 5.86: 145341 Nonbonded interactions: 377034 Sorted by model distance: nonbonded pdb=" O LEU B 123 " pdb=" HG1 THR B 126 " model vdw 1.784 1.850 nonbonded pdb=" O LEU A 123 " pdb=" HG1 THR A 126 " model vdw 1.784 1.850 nonbonded pdb=" OD1 ASP A 266 " pdb="HH21 ARG B 35 " model vdw 1.812 1.850 nonbonded pdb=" O ALA A 93 " pdb=" HG1 THR A 96 " model vdw 1.812 1.850 nonbonded pdb=" O ALA B 93 " pdb=" HG1 THR B 96 " model vdw 1.813 1.850 ... (remaining 377029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 701 through 702)) 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: 0.010 Normalize map: mean=0, sd=1: 0.050 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: 0.130 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 45.590 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 0.038 5838 Z= 0.170 Angle : 0.510 4.479 7956 Z= 0.278 Chirality : 0.033 0.134 978 Planarity : 0.004 0.038 976 Dihedral : 15.734 84.831 2040 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.26 % Allowed : 10.32 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 726 helix: 1.59 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 394 HIS 0.003 0.001 HIS B 328 PHE 0.053 0.001 PHE A 295 TYR 0.008 0.001 TYR A 313 ARG 0.001 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 ARG cc_start: 0.8477 (mtp180) cc_final: 0.8276 (mtp180) REVERT: B 335 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8301 (mtp180) REVERT: B 418 LEU cc_start: 0.8247 (tp) cc_final: 0.7967 (mp) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.3808 time to fit residues: 70.1904 Evaluate side-chains 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS B 333 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5838 Z= 0.310 Angle : 0.572 5.638 7956 Z= 0.295 Chirality : 0.037 0.132 978 Planarity : 0.005 0.043 976 Dihedral : 7.085 55.381 804 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.87 % Allowed : 13.71 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.30), residues: 726 helix: 2.81 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -0.93 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.007 0.002 HIS A 328 PHE 0.019 0.002 PHE B 99 TYR 0.012 0.002 TYR A 313 ARG 0.003 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.990 Fit side-chains REVERT: A 77 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7969 (mtt90) REVERT: A 125 TYR cc_start: 0.9269 (t80) cc_final: 0.8991 (t80) REVERT: B 77 ARG cc_start: 0.8246 (mtt90) cc_final: 0.8046 (mtt90) REVERT: B 117 MET cc_start: 0.7873 (mmp) cc_final: 0.7609 (mmt) REVERT: B 125 TYR cc_start: 0.9244 (t80) cc_final: 0.9021 (t80) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.3800 time to fit residues: 59.3408 Evaluate side-chains 113 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5838 Z= 0.320 Angle : 0.528 4.611 7956 Z= 0.275 Chirality : 0.036 0.133 978 Planarity : 0.004 0.047 976 Dihedral : 6.605 57.573 802 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.52 % Allowed : 14.03 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.30), residues: 726 helix: 2.90 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -1.00 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.016 0.002 PHE B 99 TYR 0.013 0.002 TYR B 160 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.834 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 121 average time/residue: 0.3717 time to fit residues: 60.3586 Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 166 HIS B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5838 Z= 0.161 Angle : 0.467 4.007 7956 Z= 0.236 Chirality : 0.034 0.121 978 Planarity : 0.004 0.046 976 Dihedral : 5.846 58.034 800 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.19 % Allowed : 15.00 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.31), residues: 726 helix: 3.25 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.56 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 394 HIS 0.004 0.001 HIS B 166 PHE 0.015 0.001 PHE B 99 TYR 0.012 0.002 TYR B 160 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 282 GLU cc_start: 0.4116 (mm-30) cc_final: 0.3468 (mm-30) outliers start: 26 outliers final: 23 residues processed: 116 average time/residue: 0.3602 time to fit residues: 55.3465 Evaluate side-chains 117 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5838 Z= 0.265 Angle : 0.501 4.138 7956 Z= 0.261 Chirality : 0.036 0.128 978 Planarity : 0.004 0.043 976 Dihedral : 5.225 58.992 790 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.35 % Allowed : 14.52 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.31), residues: 726 helix: 3.17 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.78 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.015 0.001 PHE B 99 TYR 0.009 0.002 TYR B 426 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.3973 (mm-30) cc_final: 0.3331 (mm-30) REVERT: B 282 GLU cc_start: 0.4159 (mm-30) cc_final: 0.3510 (mm-30) outliers start: 27 outliers final: 25 residues processed: 111 average time/residue: 0.3688 time to fit residues: 54.0839 Evaluate side-chains 117 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5838 Z= 0.163 Angle : 0.459 4.100 7956 Z= 0.234 Chirality : 0.034 0.125 978 Planarity : 0.004 0.045 976 Dihedral : 4.946 58.448 788 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.87 % Allowed : 14.68 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.31), residues: 726 helix: 3.32 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.49 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 394 HIS 0.003 0.001 HIS B 328 PHE 0.013 0.001 PHE A 99 TYR 0.008 0.002 TYR B 160 ARG 0.001 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4097 (mm-30) cc_final: 0.3202 (mm-30) REVERT: B 282 GLU cc_start: 0.4108 (mm-30) cc_final: 0.3245 (mm-30) outliers start: 24 outliers final: 24 residues processed: 114 average time/residue: 0.3526 time to fit residues: 53.4062 Evaluate side-chains 121 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5838 Z= 0.180 Angle : 0.464 4.114 7956 Z= 0.237 Chirality : 0.034 0.124 978 Planarity : 0.004 0.044 976 Dihedral : 4.853 58.440 786 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.71 % Allowed : 14.84 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.31), residues: 726 helix: 3.37 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.40 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.003 0.001 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.008 0.002 TYR B 160 ARG 0.002 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4128 (mm-30) cc_final: 0.3251 (mm-30) REVERT: B 282 GLU cc_start: 0.4016 (mm-30) cc_final: 0.3400 (mm-30) outliers start: 23 outliers final: 22 residues processed: 112 average time/residue: 0.3623 time to fit residues: 53.8192 Evaluate side-chains 116 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5838 Z= 0.186 Angle : 0.465 4.186 7956 Z= 0.238 Chirality : 0.034 0.122 978 Planarity : 0.004 0.044 976 Dihedral : 4.733 58.375 784 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.55 % Allowed : 15.32 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.31), residues: 726 helix: 3.38 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.35 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.003 0.001 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.007 0.002 TYR A 426 ARG 0.001 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4136 (mm-30) cc_final: 0.3265 (mm-30) REVERT: B 282 GLU cc_start: 0.4137 (mm-30) cc_final: 0.3260 (mm-30) outliers start: 22 outliers final: 21 residues processed: 112 average time/residue: 0.3489 time to fit residues: 52.1947 Evaluate side-chains 116 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5838 Z= 0.223 Angle : 0.481 4.326 7956 Z= 0.249 Chirality : 0.034 0.122 978 Planarity : 0.004 0.043 976 Dihedral : 4.764 58.604 784 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.39 % Allowed : 15.65 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.22 (0.31), residues: 726 helix: 3.32 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.39 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.014 0.001 PHE B 99 TYR 0.008 0.002 TYR A 426 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.912 Fit side-chains REVERT: A 282 GLU cc_start: 0.4116 (mm-30) cc_final: 0.3227 (mm-30) REVERT: B 282 GLU cc_start: 0.4122 (mm-30) cc_final: 0.3251 (mm-30) outliers start: 21 outliers final: 21 residues processed: 108 average time/residue: 0.3743 time to fit residues: 54.6249 Evaluate side-chains 114 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5838 Z= 0.151 Angle : 0.463 5.627 7956 Z= 0.235 Chirality : 0.034 0.122 978 Planarity : 0.004 0.044 976 Dihedral : 4.681 57.924 784 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.06 % Allowed : 16.61 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.31), residues: 726 helix: 3.54 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.35 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 394 HIS 0.002 0.001 HIS A 328 PHE 0.011 0.001 PHE B 99 TYR 0.006 0.002 TYR A 426 ARG 0.001 0.000 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4083 (mm-30) cc_final: 0.3226 (mm-30) REVERT: B 282 GLU cc_start: 0.4080 (mm-30) cc_final: 0.3238 (mm-30) outliers start: 19 outliers final: 19 residues processed: 110 average time/residue: 0.3649 time to fit residues: 53.3214 Evaluate side-chains 112 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.168568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118285 restraints weight = 9853.210| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.67 r_work: 0.3057 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5838 Z= 0.166 Angle : 0.468 5.044 7956 Z= 0.238 Chirality : 0.034 0.122 978 Planarity : 0.004 0.044 976 Dihedral : 4.666 57.957 784 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.06 % Allowed : 16.94 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.52 (0.31), residues: 726 helix: 3.53 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.35 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 PHE 0.012 0.001 PHE B 99 TYR 0.007 0.002 TYR A 426 ARG 0.001 0.000 ARG B 77 =============================================================================== Job complete usr+sys time: 2831.88 seconds wall clock time: 50 minutes 27.06 seconds (3027.06 seconds total)