Starting phenix.real_space_refine on Tue Apr 29 11:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fac_50272/04_2025/9fac_50272_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fac_50272/04_2025/9fac_50272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fac_50272/04_2025/9fac_50272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fac_50272/04_2025/9fac_50272.map" model { file = "/net/cci-nas-00/data/ceres_data/9fac_50272/04_2025/9fac_50272_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fac_50272/04_2025/9fac_50272_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2770 2.51 5 N 725 2.21 5 O 900 1.98 5 H 4190 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8595 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "C" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "D" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "E" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.58, per 1000 atoms: 0.65 Number of scatterers: 8595 At special positions: 0 Unit cell: (89.789, 120.904, 42.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 900 8.00 N 725 7.00 C 2770 6.00 H 4190 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 201 " - " ASN A 19 " " NAG B 201 " - " ASN B 19 " " NAG C 201 " - " ASN C 19 " " NAG D 201 " - " ASN D 19 " " NAG E 201 " - " ASN E 19 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 739.2 milliseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 13 sheets defined 4.3% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.789A pdb=" N THR A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.785A pdb=" N THR B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.700A pdb=" N THR C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.765A pdb=" N THR D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.585A pdb=" N THR E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.270A pdb=" N GLU B 3 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.421A pdb=" N VAL A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23 removed outlier: 6.771A pdb=" N ALA A 18 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR C 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER C 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS A 22 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 18 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR E 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 20 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N SER E 23 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS C 22 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.817A pdb=" N TYR B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU D 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B 28 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU B 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY A 28 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 27 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR C 30 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU A 29 " --> pdb=" O THR C 30 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.541A pdb=" N GLN A 36 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN C 36 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 51 removed outlier: 6.726A pdb=" N VAL B 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE D 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLN D 49 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR B 48 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N SER D 51 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER B 50 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE B 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLN B 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 48 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N SER B 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER A 50 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.127A pdb=" N THR B 73 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR A 73 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER E 75 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 74 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 86 removed outlier: 6.612A pdb=" N ALA B 83 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE D 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR B 85 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 83 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE B 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A 85 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.831A pdb=" N ALA B 89 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 91 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP A 90 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP C 90 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 95 through 97 removed outlier: 5.482A pdb=" N VAL B 96 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL A 96 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 96 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 96 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 107 removed outlier: 6.806A pdb=" N LEU A 103 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 105 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 103 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 105 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.691A pdb=" N LYS B 110 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS A 110 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 77 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4190 1.03 - 1.23: 28 1.23 - 1.42: 1902 1.42 - 1.62: 2575 1.62 - 1.82: 10 Bond restraints: 8705 Sorted by residual: bond pdb=" C THR D 69 " pdb=" N ALA D 70 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.40e-02 5.10e+03 2.41e+00 bond pdb=" C THR B 69 " pdb=" N ALA B 70 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.40e-02 5.10e+03 2.21e+00 bond pdb=" CB ASP E 84 " pdb=" CG ASP E 84 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.16e+00 bond pdb=" N THR B 69 " pdb=" CA THR B 69 " ideal model delta sigma weight residual 1.455 1.473 -0.018 1.27e-02 6.20e+03 2.03e+00 bond pdb=" CB TRP E 34 " pdb=" CG TRP E 34 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.02e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 14692 1.65 - 3.30: 802 3.30 - 4.95: 114 4.95 - 6.60: 36 6.60 - 8.26: 6 Bond angle restraints: 15650 Sorted by residual: angle pdb=" C ARG C 53 " pdb=" CA ARG C 53 " pdb=" CB ARG C 53 " ideal model delta sigma weight residual 110.81 105.47 5.34 1.27e+00 6.20e-01 1.77e+01 angle pdb=" C ARG A 53 " pdb=" CA ARG A 53 " pdb=" CB ARG A 53 " ideal model delta sigma weight residual 110.81 105.70 5.11 1.27e+00 6.20e-01 1.62e+01 angle pdb=" C ARG E 53 " pdb=" CA ARG E 53 " pdb=" CB ARG E 53 " ideal model delta sigma weight residual 110.81 105.97 4.84 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ALA E 18 " pdb=" CA ALA E 18 " pdb=" C ALA E 18 " ideal model delta sigma weight residual 108.69 115.08 -6.39 1.77e+00 3.19e-01 1.30e+01 angle pdb=" N GLY E 63 " pdb=" CA GLY E 63 " pdb=" C GLY E 63 " ideal model delta sigma weight residual 113.18 104.92 8.26 2.37e+00 1.78e-01 1.21e+01 ... (remaining 15645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 3631 13.29 - 26.58: 385 26.58 - 39.86: 114 39.86 - 53.15: 83 53.15 - 66.44: 82 Dihedral angle restraints: 4295 sinusoidal: 2375 harmonic: 1920 Sorted by residual: dihedral pdb=" CA ALA B 70 " pdb=" C ALA B 70 " pdb=" N THR B 71 " pdb=" CA THR B 71 " ideal model delta harmonic sigma weight residual -180.00 -164.19 -15.81 0 5.00e+00 4.00e-02 9.99e+00 dihedral pdb=" CA ALA A 70 " pdb=" C ALA A 70 " pdb=" N THR A 71 " pdb=" CA THR A 71 " ideal model delta harmonic sigma weight residual -180.00 -164.34 -15.66 0 5.00e+00 4.00e-02 9.81e+00 dihedral pdb=" CA ALA C 70 " pdb=" C ALA C 70 " pdb=" N THR C 71 " pdb=" CA THR C 71 " ideal model delta harmonic sigma weight residual -180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 4292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 585 0.082 - 0.165: 107 0.165 - 0.247: 3 0.247 - 0.329: 1 0.329 - 0.411: 4 Chirality restraints: 700 Sorted by residual: chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 19 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C1 NAG E 201 " pdb=" ND2 ASN E 19 " pdb=" C2 NAG E 201 " pdb=" O5 NAG E 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 697 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 90 " -0.007 2.00e-02 2.50e+03 1.30e-02 6.81e+00 pdb=" CG TRP B 90 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP B 90 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 90 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 90 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP B 90 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 90 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 90 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 90 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 90 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 90 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP B 90 " 0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP B 90 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 90 " 0.010 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 90 " -0.016 2.00e-02 2.50e+03 pdb=" HH2 TRP B 90 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 90 " -0.006 2.00e-02 2.50e+03 1.29e-02 6.66e+00 pdb=" CG TRP E 90 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP E 90 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 90 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 90 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP E 90 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 90 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 90 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 90 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 90 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP E 90 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP E 90 " 0.023 2.00e-02 2.50e+03 pdb=" HE3 TRP E 90 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 90 " 0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 90 " -0.016 2.00e-02 2.50e+03 pdb=" HH2 TRP E 90 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 90 " -0.004 2.00e-02 2.50e+03 1.28e-02 6.56e+00 pdb=" CG TRP C 90 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP C 90 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 90 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 90 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP C 90 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 90 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 90 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 90 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 90 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP C 90 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP C 90 " 0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP C 90 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 90 " 0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 90 " -0.016 2.00e-02 2.50e+03 pdb=" HH2 TRP C 90 " 0.010 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 823 2.21 - 2.81: 17824 2.81 - 3.41: 21009 3.41 - 4.00: 30585 4.00 - 4.60: 43592 Nonbonded interactions: 113833 Sorted by model distance: nonbonded pdb=" OE2 GLU B 3 " pdb=" HG1 THR B 5 " model vdw 1.615 2.450 nonbonded pdb=" OE2 GLU D 3 " pdb=" HG1 THR D 5 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU C 3 " pdb=" HG1 THR C 5 " model vdw 1.632 2.450 nonbonded pdb=" HZ2 LYS C 38 " pdb=" OD2 ASP C 81 " model vdw 1.636 2.450 nonbonded pdb=" OE2 GLU E 3 " pdb=" HG1 THR E 5 " model vdw 1.637 2.450 ... (remaining 113828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.140 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.610 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 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 : 0.007 0.044 4525 Z= 0.330 Angle : 1.196 8.255 6185 Z= 0.657 Chirality : 0.066 0.411 700 Planarity : 0.009 0.063 795 Dihedral : 11.943 66.436 1675 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -4.35 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.007 TRP B 90 PHE 0.035 0.005 PHE C 86 TYR 0.020 0.005 TYR D 35 ARG 0.010 0.002 ARG D 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00866 ( 5) link_NAG-ASN : angle 4.95038 ( 15) hydrogen bonds : bond 0.22845 ( 77) hydrogen bonds : angle 8.62391 ( 216) SS BOND : bond 0.00736 ( 5) SS BOND : angle 1.44899 ( 10) covalent geometry : bond 0.00689 ( 4515) covalent geometry : angle 1.17134 ( 6160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6769 (pm20) cc_final: 0.6126 (pp30) REVERT: A 27 LEU cc_start: 0.7324 (mp) cc_final: 0.6969 (mt) REVERT: A 75 SER cc_start: 0.7308 (t) cc_final: 0.7060 (m) REVERT: A 77 THR cc_start: 0.7512 (p) cc_final: 0.7210 (m) REVERT: A 93 THR cc_start: 0.7708 (m) cc_final: 0.7505 (p) REVERT: B 16 GLN cc_start: 0.6259 (pm20) cc_final: 0.5669 (pp30) REVERT: D 6 GLN cc_start: 0.7085 (pt0) cc_final: 0.6733 (mp10) REVERT: D 16 GLN cc_start: 0.6956 (pm20) cc_final: 0.6029 (pp30) REVERT: D 52 LYS cc_start: 0.6127 (tttt) cc_final: 0.4452 (pttm) REVERT: E 52 LYS cc_start: 0.5994 (tttt) cc_final: 0.5631 (mtpt) REVERT: E 75 SER cc_start: 0.7304 (t) cc_final: 0.7003 (m) REVERT: E 82 GLU cc_start: 0.7323 (mm-30) cc_final: 0.5805 (pp20) REVERT: E 93 THR cc_start: 0.8219 (m) cc_final: 0.7898 (p) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3144 time to fit residues: 53.6662 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 49 GLN A 65 ASN B 6 GLN B 49 GLN B 65 ASN C 6 GLN C 65 ASN D 6 GLN D 49 GLN E 65 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.162086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.144424 restraints weight = 25952.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.148566 restraints weight = 11782.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.151106 restraints weight = 6768.230| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4525 Z= 0.138 Angle : 0.723 6.376 6185 Z= 0.368 Chirality : 0.055 0.349 700 Planarity : 0.007 0.042 795 Dihedral : 6.419 29.057 725 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.44 % Allowed : 11.34 % Favored : 87.22 % 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: -3.97 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 PHE 0.012 0.001 PHE A 2 TYR 0.010 0.001 TYR A 26 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 5) link_NAG-ASN : angle 4.67695 ( 15) hydrogen bonds : bond 0.04713 ( 77) hydrogen bonds : angle 6.21929 ( 216) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.64979 ( 10) covalent geometry : bond 0.00303 ( 4515) covalent geometry : angle 0.68652 ( 6160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6544 (pm20) cc_final: 0.6319 (pp30) REVERT: B 16 GLN cc_start: 0.5987 (pm20) cc_final: 0.5747 (pp30) REVERT: B 78 GLN cc_start: 0.7721 (tt0) cc_final: 0.7448 (tt0) REVERT: C 77 THR cc_start: 0.7408 (p) cc_final: 0.7157 (m) REVERT: D 52 LYS cc_start: 0.6194 (tttt) cc_final: 0.4617 (pttm) REVERT: E 52 LYS cc_start: 0.5965 (tttt) cc_final: 0.5631 (mtpt) REVERT: E 75 SER cc_start: 0.7468 (t) cc_final: 0.7221 (m) REVERT: E 82 GLU cc_start: 0.7240 (mm-30) cc_final: 0.5895 (pp20) REVERT: E 93 THR cc_start: 0.8329 (m) cc_final: 0.8049 (p) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.2864 time to fit residues: 39.6738 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.161146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.143361 restraints weight = 26174.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.147566 restraints weight = 12080.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.150030 restraints weight = 6896.821| |-----------------------------------------------------------------------------| r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4525 Z= 0.127 Angle : 0.636 5.287 6185 Z= 0.321 Chirality : 0.053 0.307 700 Planarity : 0.007 0.046 795 Dihedral : 5.918 20.961 725 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.65 % Allowed : 13.61 % Favored : 84.74 % 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: -3.77 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 34 PHE 0.012 0.001 PHE C 61 TYR 0.009 0.001 TYR E 31 ARG 0.001 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 5) link_NAG-ASN : angle 3.75874 ( 15) hydrogen bonds : bond 0.03852 ( 77) hydrogen bonds : angle 5.69403 ( 216) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.45155 ( 10) covalent geometry : bond 0.00279 ( 4515) covalent geometry : angle 0.60989 ( 6160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6567 (pm20) cc_final: 0.6334 (pp30) REVERT: A 65 ASN cc_start: 0.2867 (OUTLIER) cc_final: 0.2556 (m110) REVERT: A 80 LEU cc_start: 0.8079 (mp) cc_final: 0.7799 (mp) REVERT: B 82 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7363 (mm-30) REVERT: D 16 GLN cc_start: 0.6732 (pm20) cc_final: 0.6319 (pp30) REVERT: D 52 LYS cc_start: 0.6410 (tttt) cc_final: 0.4652 (pttm) REVERT: E 52 LYS cc_start: 0.6164 (tttt) cc_final: 0.5819 (mtpt) REVERT: E 75 SER cc_start: 0.7651 (t) cc_final: 0.7402 (m) REVERT: E 82 GLU cc_start: 0.7245 (mm-30) cc_final: 0.5924 (pp20) REVERT: E 93 THR cc_start: 0.8365 (m) cc_final: 0.8122 (p) outliers start: 8 outliers final: 4 residues processed: 103 average time/residue: 0.2954 time to fit residues: 39.8565 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4696 r_free = 0.4696 target = 0.161040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.144721 restraints weight = 26090.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.148496 restraints weight = 12195.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.150779 restraints weight = 7095.035| |-----------------------------------------------------------------------------| r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4525 Z= 0.134 Angle : 0.611 5.540 6185 Z= 0.309 Chirality : 0.052 0.304 700 Planarity : 0.007 0.046 795 Dihedral : 5.793 21.699 725 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.86 % Allowed : 14.43 % Favored : 83.71 % 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: -3.72 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 34 PHE 0.008 0.001 PHE C 61 TYR 0.009 0.001 TYR E 31 ARG 0.001 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 5) link_NAG-ASN : angle 3.32617 ( 15) hydrogen bonds : bond 0.03110 ( 77) hydrogen bonds : angle 5.38712 ( 216) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.46569 ( 10) covalent geometry : bond 0.00297 ( 4515) covalent geometry : angle 0.58936 ( 6160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6703 (pm20) cc_final: 0.6483 (pp30) REVERT: A 65 ASN cc_start: 0.2586 (OUTLIER) cc_final: 0.2307 (m110) REVERT: B 82 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 16 GLN cc_start: 0.6875 (pm20) cc_final: 0.6425 (pp30) REVERT: D 52 LYS cc_start: 0.6513 (tttt) cc_final: 0.4747 (pttm) REVERT: E 75 SER cc_start: 0.7853 (t) cc_final: 0.7624 (m) REVERT: E 82 GLU cc_start: 0.7193 (mm-30) cc_final: 0.5946 (pp20) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.2916 time to fit residues: 39.0475 Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.161320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.144846 restraints weight = 26081.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.148641 restraints weight = 12239.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.150938 restraints weight = 7156.341| |-----------------------------------------------------------------------------| r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4525 Z= 0.121 Angle : 0.585 5.061 6185 Z= 0.294 Chirality : 0.051 0.293 700 Planarity : 0.007 0.043 795 Dihedral : 5.555 21.004 725 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.27 % Allowed : 15.05 % Favored : 82.68 % 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: -3.69 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 34 PHE 0.013 0.001 PHE B 61 TYR 0.009 0.001 TYR E 31 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 3.03322 ( 15) hydrogen bonds : bond 0.02828 ( 77) hydrogen bonds : angle 5.20750 ( 216) SS BOND : bond 0.00289 ( 5) SS BOND : angle 0.42650 ( 10) covalent geometry : bond 0.00276 ( 4515) covalent geometry : angle 0.56613 ( 6160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6720 (pm20) cc_final: 0.6434 (pp30) REVERT: A 65 ASN cc_start: 0.2631 (OUTLIER) cc_final: 0.2308 (m110) REVERT: B 82 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7050 (mm-30) REVERT: D 16 GLN cc_start: 0.6916 (pm20) cc_final: 0.6252 (pp30) REVERT: D 52 LYS cc_start: 0.6517 (tttt) cc_final: 0.4773 (pttm) REVERT: D 82 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 75 SER cc_start: 0.7900 (t) cc_final: 0.7693 (m) REVERT: E 82 GLU cc_start: 0.7217 (mm-30) cc_final: 0.5969 (pp20) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.2918 time to fit residues: 38.6371 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.161966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.145205 restraints weight = 25825.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.149011 restraints weight = 12313.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.151316 restraints weight = 7245.104| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4525 Z= 0.108 Angle : 0.556 5.153 6185 Z= 0.279 Chirality : 0.051 0.280 700 Planarity : 0.006 0.042 795 Dihedral : 5.440 20.162 725 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.65 % Allowed : 15.46 % Favored : 82.89 % 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: -3.63 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 34 PHE 0.012 0.001 PHE B 61 TYR 0.009 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 5) link_NAG-ASN : angle 2.80571 ( 15) hydrogen bonds : bond 0.02824 ( 77) hydrogen bonds : angle 5.06905 ( 216) SS BOND : bond 0.00139 ( 5) SS BOND : angle 0.84556 ( 10) covalent geometry : bond 0.00249 ( 4515) covalent geometry : angle 0.53820 ( 6160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6693 (pm20) cc_final: 0.6357 (pp30) REVERT: A 65 ASN cc_start: 0.2418 (OUTLIER) cc_final: 0.2116 (m110) REVERT: B 82 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7073 (mm-30) REVERT: C 16 GLN cc_start: 0.6622 (pp30) cc_final: 0.6252 (pp30) REVERT: D 16 GLN cc_start: 0.6923 (pm20) cc_final: 0.6386 (pp30) REVERT: D 52 LYS cc_start: 0.6538 (tttt) cc_final: 0.4806 (pttm) REVERT: E 82 GLU cc_start: 0.7211 (mm-30) cc_final: 0.5981 (pp20) outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 0.3127 time to fit residues: 39.9029 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4707 r_free = 0.4707 target = 0.160745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.143795 restraints weight = 26563.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.147641 restraints weight = 12791.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.149936 restraints weight = 7530.176| |-----------------------------------------------------------------------------| r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4525 Z= 0.117 Angle : 0.550 5.103 6185 Z= 0.275 Chirality : 0.050 0.273 700 Planarity : 0.006 0.040 795 Dihedral : 5.384 21.097 725 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.47 % Allowed : 15.46 % Favored : 82.06 % 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: -3.67 (0.26), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 PHE 0.016 0.001 PHE B 61 TYR 0.011 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 2.56808 ( 15) hydrogen bonds : bond 0.02514 ( 77) hydrogen bonds : angle 4.86496 ( 216) SS BOND : bond 0.00149 ( 5) SS BOND : angle 0.62016 ( 10) covalent geometry : bond 0.00269 ( 4515) covalent geometry : angle 0.53578 ( 6160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6747 (pm20) cc_final: 0.6374 (pp30) REVERT: A 65 ASN cc_start: 0.2214 (OUTLIER) cc_final: 0.1929 (m110) REVERT: B 82 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7088 (mm-30) REVERT: C 16 GLN cc_start: 0.6742 (pp30) cc_final: 0.6484 (pp30) REVERT: D 16 GLN cc_start: 0.6948 (pm20) cc_final: 0.6369 (pp30) REVERT: D 52 LYS cc_start: 0.6595 (tttt) cc_final: 0.4850 (pttm) REVERT: E 82 GLU cc_start: 0.7218 (mm-30) cc_final: 0.5999 (pt0) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.2887 time to fit residues: 38.2365 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.160854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.144294 restraints weight = 26446.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.148032 restraints weight = 12561.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.150390 restraints weight = 7455.664| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4525 Z= 0.118 Angle : 0.550 5.098 6185 Z= 0.275 Chirality : 0.051 0.275 700 Planarity : 0.006 0.039 795 Dihedral : 5.385 21.253 725 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.27 % Allowed : 15.67 % Favored : 82.06 % 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: -3.70 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 PHE 0.013 0.001 PHE E 61 TYR 0.011 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 2.52923 ( 15) hydrogen bonds : bond 0.02432 ( 77) hydrogen bonds : angle 4.76714 ( 216) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.61410 ( 10) covalent geometry : bond 0.00269 ( 4515) covalent geometry : angle 0.53667 ( 6160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6838 (pm20) cc_final: 0.6408 (pp30) REVERT: A 65 ASN cc_start: 0.2153 (OUTLIER) cc_final: 0.1851 (m110) REVERT: C 16 GLN cc_start: 0.6831 (pp30) cc_final: 0.6584 (pp30) REVERT: D 16 GLN cc_start: 0.7159 (pm20) cc_final: 0.6341 (pp30) REVERT: D 52 LYS cc_start: 0.6759 (tttt) cc_final: 0.4961 (pttm) REVERT: E 82 GLU cc_start: 0.7207 (mm-30) cc_final: 0.5979 (pt0) outliers start: 11 outliers final: 10 residues processed: 98 average time/residue: 0.2642 time to fit residues: 34.9018 Evaluate side-chains 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.163022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.146345 restraints weight = 26120.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.150191 restraints weight = 12287.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.152556 restraints weight = 7180.653| |-----------------------------------------------------------------------------| r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4525 Z= 0.126 Angle : 0.556 5.096 6185 Z= 0.278 Chirality : 0.050 0.280 700 Planarity : 0.006 0.039 795 Dihedral : 5.451 22.700 725 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.47 % Allowed : 15.26 % Favored : 82.27 % 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 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 90 PHE 0.012 0.001 PHE E 61 TYR 0.011 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 5) link_NAG-ASN : angle 2.47345 ( 15) hydrogen bonds : bond 0.02429 ( 77) hydrogen bonds : angle 4.69802 ( 216) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.66158 ( 10) covalent geometry : bond 0.00284 ( 4515) covalent geometry : angle 0.54247 ( 6160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6850 (pm20) cc_final: 0.6434 (pp30) REVERT: A 65 ASN cc_start: 0.2093 (OUTLIER) cc_final: 0.1759 (m110) REVERT: D 16 GLN cc_start: 0.7184 (pm20) cc_final: 0.6372 (pp30) REVERT: D 52 LYS cc_start: 0.6750 (tttt) cc_final: 0.4984 (pttm) REVERT: E 82 GLU cc_start: 0.7221 (mm-30) cc_final: 0.5963 (pt0) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.2802 time to fit residues: 37.4211 Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.143951 restraints weight = 25949.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.147654 restraints weight = 12479.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.150072 restraints weight = 7389.427| |-----------------------------------------------------------------------------| r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4525 Z= 0.122 Angle : 0.554 5.038 6185 Z= 0.276 Chirality : 0.050 0.278 700 Planarity : 0.006 0.039 795 Dihedral : 5.419 22.294 725 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.06 % Allowed : 16.08 % Favored : 81.86 % 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: -3.80 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 90 PHE 0.012 0.001 PHE E 61 TYR 0.013 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 5) link_NAG-ASN : angle 2.47913 ( 15) hydrogen bonds : bond 0.02385 ( 77) hydrogen bonds : angle 4.69342 ( 216) SS BOND : bond 0.00246 ( 5) SS BOND : angle 1.23141 ( 10) covalent geometry : bond 0.00280 ( 4515) covalent geometry : angle 0.53941 ( 6160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6846 (pm20) cc_final: 0.6447 (pp30) REVERT: A 65 ASN cc_start: 0.2148 (OUTLIER) cc_final: 0.1793 (m110) REVERT: D 16 GLN cc_start: 0.7193 (pm20) cc_final: 0.6339 (pp30) REVERT: D 52 LYS cc_start: 0.6785 (tttt) cc_final: 0.4997 (pttm) REVERT: E 82 GLU cc_start: 0.7220 (mm-30) cc_final: 0.5994 (pt0) outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 0.2723 time to fit residues: 35.9050 Evaluate side-chains 100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.156698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.138631 restraints weight = 27053.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.142977 restraints weight = 12450.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.145621 restraints weight = 7204.171| |-----------------------------------------------------------------------------| r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4525 Z= 0.152 Angle : 0.600 5.488 6185 Z= 0.301 Chirality : 0.051 0.296 700 Planarity : 0.006 0.040 795 Dihedral : 5.862 26.557 725 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.27 % Allowed : 16.29 % Favored : 81.44 % 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: -4.03 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 90 PHE 0.015 0.002 PHE E 61 TYR 0.015 0.002 TYR A 26 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 5) link_NAG-ASN : angle 2.54265 ( 15) hydrogen bonds : bond 0.02683 ( 77) hydrogen bonds : angle 4.75022 ( 216) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.04215 ( 10) covalent geometry : bond 0.00338 ( 4515) covalent geometry : angle 0.58607 ( 6160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.20 seconds wall clock time: 70 minutes 31.79 seconds (4231.79 seconds total)