Starting phenix.real_space_refine (version: dev) on Mon Feb 20 06:32:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/02_2023/6wcc_21606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/02_2023/6wcc_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_21606/02_2023/6wcc_21606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/02_2023/6wcc_21606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/02_2023/6wcc_21606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/02_2023/6wcc_21606.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 6.12, per 1000 atoms: 0.53 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: 9.79 Conformation dependent library (CDL) restraints added in 923.9 milliseconds 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: 0.23 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: 4.52 Time building geometry restraints manager: 10.12 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: 4226 16.97 - 33.93: 396 33.93 - 50.90: 80 50.90 - 67.86: 30 67.86 - 84.83: 6 Dihedral angle restraints: 4738 sinusoidal: 2146 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 4735 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.170 Extract box with map and model: 1.430 Check model and map are aligned: 0.170 Process input model: 44.300 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 % 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 *********************** 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 : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.4078 time to fit residues: 75.4202 Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1398 time to fit residues: 4.1141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 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 333 HIS B 333 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 5838 Z= 0.327 Angle : 0.551 4.612 7956 Z= 0.288 Chirality : 0.037 0.129 978 Planarity : 0.004 0.044 976 Dihedral : 3.453 18.116 780 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 2.58 % 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: 3.15 (0.30), residues: 726 helix: 2.75 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 140 *********************** 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 118 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.4159 time to fit residues: 62.6351 Evaluate side-chains 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1409 time to fit residues: 4.2428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7749 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 5838 Z= 0.237 Angle : 0.503 4.384 7956 Z= 0.259 Chirality : 0.035 0.127 978 Planarity : 0.004 0.047 976 Dihedral : 3.402 18.950 780 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.29 % 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: 3.58 (0.30), residues: 726 helix: 2.99 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.92 (0.51), residues: 128 *********************** 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 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 0.3837 time to fit residues: 52.6303 Evaluate side-chains 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1319 time to fit residues: 2.5276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 5838 Z= 0.245 Angle : 0.498 4.114 7956 Z= 0.258 Chirality : 0.035 0.124 978 Planarity : 0.004 0.045 976 Dihedral : 3.347 18.423 780 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.29 % 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: 3.76 (0.31), residues: 726 helix: 3.09 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.73 (0.53), residues: 128 *********************** 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 100 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.791 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 0.4079 time to fit residues: 51.3841 Evaluate side-chains 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1451 time to fit residues: 3.1249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 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: 4.9990 chunk 17 optimal weight: 5.9990 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 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 5838 Z= 0.322 Angle : 0.531 4.430 7956 Z= 0.278 Chirality : 0.036 0.135 978 Planarity : 0.004 0.044 976 Dihedral : 3.479 19.299 780 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.81 % 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: 3.57 (0.31), residues: 726 helix: 2.94 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.65 (0.54), residues: 128 *********************** 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 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.791 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 96 average time/residue: 0.4125 time to fit residues: 51.6632 Evaluate side-chains 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1473 time to fit residues: 2.2102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 5838 Z= 0.170 Angle : 0.474 4.087 7956 Z= 0.241 Chirality : 0.034 0.124 978 Planarity : 0.004 0.045 976 Dihedral : 3.325 18.702 780 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.48 % 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: 4.10 (0.31), residues: 726 helix: 3.27 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.41 (0.55), residues: 124 *********************** 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 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.940 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 97 average time/residue: 0.3975 time to fit residues: 50.4554 Evaluate side-chains 98 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1307 time to fit residues: 1.8313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.7754 moved from start: 0.3595 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= 0.224 Angle : 0.489 4.229 7956 Z= 0.252 Chirality : 0.035 0.124 978 Planarity : 0.004 0.045 976 Dihedral : 3.325 19.391 780 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.32 % 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: 4.05 (0.31), residues: 726 helix: 3.20 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.36 (0.57), residues: 120 *********************** 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 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.903 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.4070 time to fit residues: 50.0313 Evaluate side-chains 92 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1256 time to fit residues: 1.3028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.3735 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= 0.273 Angle : 0.508 4.294 7956 Z= 0.264 Chirality : 0.035 0.127 978 Planarity : 0.004 0.044 976 Dihedral : 3.400 19.315 780 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.48 % 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: 3.88 (0.31), residues: 726 helix: 3.08 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.39 (0.58), residues: 120 *********************** 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 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.960 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 95 average time/residue: 0.4156 time to fit residues: 52.2133 Evaluate side-chains 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5838 Z= 0.245 Angle : 0.506 5.271 7956 Z= 0.261 Chirality : 0.035 0.123 978 Planarity : 0.004 0.043 976 Dihedral : 3.372 18.985 780 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.16 % 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: 3.96 (0.31), residues: 726 helix: 3.14 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.37 (0.59), residues: 120 *********************** 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 92 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.4061 time to fit residues: 48.5415 Evaluate side-chains 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5838 Z= 0.217 Angle : 0.496 4.695 7956 Z= 0.254 Chirality : 0.034 0.121 978 Planarity : 0.004 0.044 976 Dihedral : 3.321 18.764 780 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.16 % 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: 4.06 (0.31), residues: 726 helix: 3.21 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.39 (0.59), residues: 120 ********************** 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 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.979 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.4247 time to fit residues: 50.6786 Evaluate side-chains 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1231 time to fit residues: 1.3997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.165789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114721 restraints weight = 9771.892| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.69 r_work: 0.3007 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5838 Z= 0.247 Angle : 0.507 4.561 7956 Z= 0.261 Chirality : 0.035 0.123 978 Planarity : 0.004 0.043 976 Dihedral : 3.346 18.435 780 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.32 % 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: 3.98 (0.31), residues: 726 helix: 3.15 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.36 (0.60), residues: 120 =============================================================================== Job complete usr+sys time: 2694.08 seconds wall clock time: 48 minutes 36.57 seconds (2916.57 seconds total)