Starting phenix.real_space_refine on Mon May 12 02:13:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fac_50272/05_2025/9fac_50272_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fac_50272/05_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_50272/05_2025/9fac_50272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fac_50272/05_2025/9fac_50272.map" model { file = "/net/cci-nas-00/data/ceres_data/9fac_50272/05_2025/9fac_50272_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fac_50272/05_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-5687/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: 5.04, per 1000 atoms: 0.59 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: 2.24 Conformation dependent library (CDL) restraints added in 779.0 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: 0.88 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: 2.95 Time building geometry restraints manager: 2.66 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: 0.04 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: 2.100 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: 0.150 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.390 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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 : 0.688 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: 0.3116 time to fit residues: 53.1485 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 : 0.598 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.7182 ------------------------------------------------------------------------------- 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 49 GLN E 65 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.162210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.144427 restraints weight = 25961.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.148592 restraints weight = 11650.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.151069 restraints weight = 6679.396| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4525 Z= 0.137 Angle : 0.721 6.328 6185 Z= 0.368 Chirality : 0.055 0.346 700 Planarity : 0.007 0.043 795 Dihedral : 6.366 28.738 725 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -3.98 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 34 PHE 0.012 0.001 PHE A 2 TYR 0.010 0.001 TYR A 48 ARG 0.001 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 5) link_NAG-ASN : angle 4.65563 ( 15) hydrogen bonds : bond 0.04835 ( 77) hydrogen bonds : angle 6.22092 ( 216) SS BOND : bond 0.00129 ( 5) SS BOND : angle 0.59805 ( 10) covalent geometry : bond 0.00299 ( 4515) covalent geometry : angle 0.68427 ( 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 109 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.670 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: 0.6540 (pm20) cc_final: 0.6277 (pp30) REVERT: B 78 GLN cc_start: 0.7762 (tt0) cc_final: 0.7486 (tt0) REVERT: C 77 THR cc_start: 0.7431 (p) cc_final: 0.7163 (m) REVERT: D 16 GLN cc_start: 0.6707 (pm20) cc_final: 0.6244 (pp30) REVERT: D 52 LYS cc_start: 0.6173 (tttt) cc_final: 0.4592 (pttm) REVERT: E 52 LYS cc_start: 0.5951 (tttt) cc_final: 0.5616 (mtpt) REVERT: E 75 SER cc_start: 0.7452 (t) cc_final: 0.7201 (m) REVERT: E 82 GLU cc_start: 0.7252 (mm-30) cc_final: 0.5891 (pp20) REVERT: E 93 THR cc_start: 0.8341 (m) cc_final: 0.8050 (p) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2831 time to fit residues: 39.2897 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4657 r_free = 0.4657 target = 0.160880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.142984 restraints weight = 25936.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.147088 restraints weight = 11938.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.149534 restraints weight = 6918.551| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4525 Z= 0.126 Angle : 0.632 5.385 6185 Z= 0.319 Chirality : 0.053 0.310 700 Planarity : 0.007 0.047 795 Dihedral : 5.909 21.182 725 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.65 % Allowed : 13.81 % Favored : 84.54 % 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 0.006 0.001 TRP D 34 PHE 0.012 0.001 PHE C 61 TYR 0.010 0.001 TYR E 31 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 3.69199 ( 15) hydrogen bonds : bond 0.03718 ( 77) hydrogen bonds : angle 5.65370 ( 216) SS BOND : bond 0.00174 ( 5) SS BOND : angle 0.47668 ( 10) covalent geometry : bond 0.00280 ( 4515) covalent geometry : angle 0.60642 ( 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 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.671 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: 0.6699 (pm20) cc_final: 0.6303 (pp30) REVERT: A 38 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7910 (ptpp) REVERT: A 65 ASN cc_start: 0.2841 (OUTLIER) cc_final: 0.2523 (m110) REVERT: A 80 LEU cc_start: 0.8082 (mp) cc_final: 0.7805 (mp) REVERT: D 16 GLN cc_start: 0.6702 (pm20) cc_final: 0.6336 (pp30) REVERT: D 52 LYS cc_start: 0.6419 (tttt) cc_final: 0.4655 (pttm) REVERT: E 75 SER cc_start: 0.7661 (t) cc_final: 0.7414 (m) REVERT: E 82 GLU cc_start: 0.7247 (mm-30) cc_final: 0.5927 (pp20) REVERT: E 93 THR cc_start: 0.8360 (m) cc_final: 0.8121 (p) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.2881 time to fit residues: 39.3622 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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: 3.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.161794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.145378 restraints weight = 26012.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.149186 restraints weight = 12103.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.151444 restraints weight = 7036.341| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.3310 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= 0.112 Angle : 0.582 5.432 6185 Z= 0.293 Chirality : 0.051 0.292 700 Planarity : 0.006 0.047 795 Dihedral : 5.541 19.330 725 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.06 % Allowed : 14.23 % 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: -3.67 (0.25), 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 0.005 0.001 TRP D 34 PHE 0.008 0.001 PHE C 61 TYR 0.010 0.001 TYR E 31 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 3.11177 ( 15) hydrogen bonds : bond 0.02847 ( 77) hydrogen bonds : angle 5.31847 ( 216) SS BOND : bond 0.00148 ( 5) SS BOND : angle 0.41251 ( 10) covalent geometry : bond 0.00253 ( 4515) covalent geometry : angle 0.56218 ( 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 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.687 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: 0.6748 (pm20) cc_final: 0.6470 (pp30) REVERT: A 38 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7832 (ptpp) REVERT: A 65 ASN cc_start: 0.2403 (OUTLIER) cc_final: 0.2109 (m110) REVERT: B 82 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6968 (mm-30) REVERT: D 16 GLN cc_start: 0.6908 (pm20) cc_final: 0.6460 (pp30) REVERT: D 52 LYS cc_start: 0.6475 (tttt) cc_final: 0.4719 (pttm) REVERT: E 82 GLU cc_start: 0.7218 (mm-30) cc_final: 0.5991 (pp20) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.2974 time to fit residues: 40.4155 Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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: 3.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.0050 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.162679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.145982 restraints weight = 25909.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.149817 restraints weight = 11987.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.152117 restraints weight = 7037.508| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4525 Z= 0.098 Angle : 0.546 4.779 6185 Z= 0.274 Chirality : 0.050 0.272 700 Planarity : 0.006 0.045 795 Dihedral : 5.204 18.767 725 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.27 % Allowed : 14.43 % Favored : 83.30 % 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: -3.56 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 34 PHE 0.014 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 0.00274 ( 5) link_NAG-ASN : angle 2.73134 ( 15) hydrogen bonds : bond 0.02544 ( 77) hydrogen bonds : angle 5.11113 ( 216) SS BOND : bond 0.00133 ( 5) SS BOND : angle 0.46121 ( 10) covalent geometry : bond 0.00235 ( 4515) covalent geometry : angle 0.53004 ( 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 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.616 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: 0.6699 (pm20) cc_final: 0.6404 (pp30) REVERT: A 38 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: A 65 ASN cc_start: 0.2576 (OUTLIER) cc_final: 0.2271 (m110) REVERT: B 82 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 16 GLN cc_start: 0.6928 (pm20) cc_final: 0.6393 (pp30) REVERT: D 52 LYS cc_start: 0.6510 (tttt) cc_final: 0.4780 (pttm) REVERT: D 82 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7077 (mt-10) REVERT: E 82 GLU cc_start: 0.7195 (mm-30) cc_final: 0.5961 (pp20) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.2819 time to fit residues: 37.3983 Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 38 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN ** C 88 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 = 0.4701 r_free = 0.4701 target = 0.160650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.143921 restraints weight = 25886.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.147744 restraints weight = 12210.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.150059 restraints weight = 7211.011| |-----------------------------------------------------------------------------| r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4525 Z= 0.147 Angle : 0.581 5.795 6185 Z= 0.294 Chirality : 0.051 0.285 700 Planarity : 0.006 0.049 795 Dihedral : 5.559 22.547 725 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.47 % Allowed : 15.05 % Favored : 82.47 % 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: -3.66 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 PHE 0.011 0.001 PHE E 61 TYR 0.008 0.001 TYR E 31 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 2.63778 ( 15) hydrogen bonds : bond 0.02852 ( 77) hydrogen bonds : angle 4.99273 ( 216) SS BOND : bond 0.00277 ( 5) SS BOND : angle 0.98291 ( 10) covalent geometry : bond 0.00328 ( 4515) covalent geometry : angle 0.56631 ( 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 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.686 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: 0.6762 (pm20) cc_final: 0.6378 (pp30) REVERT: A 65 ASN cc_start: 0.2467 (OUTLIER) cc_final: 0.2175 (m110) REVERT: B 82 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7035 (mm-30) REVERT: C 16 GLN cc_start: 0.6578 (pp30) cc_final: 0.6282 (pp30) REVERT: D 16 GLN cc_start: 0.6984 (pm20) cc_final: 0.6390 (pp30) REVERT: D 52 LYS cc_start: 0.6582 (tttt) cc_final: 0.4827 (pttm) REVERT: E 82 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6007 (pp20) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.3011 time to fit residues: 39.0490 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 : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A 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 71 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.161104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.144117 restraints weight = 26125.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.147892 restraints weight = 12664.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.150293 restraints weight = 7525.029| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4525 Z= 0.110 Angle : 0.548 4.424 6185 Z= 0.273 Chirality : 0.051 0.278 700 Planarity : 0.006 0.043 795 Dihedral : 5.274 20.113 725 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.47 % Allowed : 16.08 % 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: -3.63 (0.26), 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 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 0.00208 ( 5) link_NAG-ASN : angle 2.62872 ( 15) hydrogen bonds : bond 0.02488 ( 77) hydrogen bonds : angle 4.88870 ( 216) SS BOND : bond 0.00168 ( 5) SS BOND : angle 0.70398 ( 10) covalent geometry : bond 0.00255 ( 4515) covalent geometry : angle 0.53308 ( 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 : 0.719 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: 0.6764 (pm20) cc_final: 0.6362 (pp30) REVERT: A 31 TYR cc_start: 0.7904 (m-80) cc_final: 0.7694 (m-80) REVERT: A 65 ASN cc_start: 0.2228 (OUTLIER) cc_final: 0.1940 (m110) REVERT: B 82 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7081 (mm-30) REVERT: C 16 GLN cc_start: 0.6657 (pp30) cc_final: 0.6369 (pp30) REVERT: D 16 GLN cc_start: 0.6950 (pm20) cc_final: 0.6344 (pp30) REVERT: D 52 LYS cc_start: 0.6581 (tttt) cc_final: 0.4846 (pttm) REVERT: D 82 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7615 (mm-30) REVERT: E 82 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6025 (pp20) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.3080 time to fit residues: 40.3102 Evaluate side-chains 100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A 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 88 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4688 r_free = 0.4688 target = 0.159460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.142569 restraints weight = 26320.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.146335 restraints weight = 13015.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.148706 restraints weight = 7720.368| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4525 Z= 0.186 Angle : 0.628 5.809 6185 Z= 0.320 Chirality : 0.052 0.301 700 Planarity : 0.006 0.044 795 Dihedral : 5.858 25.956 725 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.68 % Allowed : 16.08 % Favored : 81.24 % 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: -3.86 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 PHE 0.014 0.001 PHE E 61 TYR 0.028 0.002 TYR C 85 ARG 0.002 0.001 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 5) link_NAG-ASN : angle 2.59408 ( 15) hydrogen bonds : bond 0.02962 ( 77) hydrogen bonds : angle 4.92790 ( 216) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.89760 ( 10) covalent geometry : bond 0.00396 ( 4515) covalent geometry : angle 0.61509 ( 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 106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 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: A 16 GLN cc_start: 0.6854 (pm20) cc_final: 0.6477 (pp30) REVERT: A 65 ASN cc_start: 0.2324 (OUTLIER) cc_final: 0.2016 (m110) REVERT: D 16 GLN cc_start: 0.7078 (pm20) cc_final: 0.6364 (pp30) REVERT: D 52 LYS cc_start: 0.6632 (tttt) cc_final: 0.4873 (pttm) REVERT: E 82 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6003 (pt0) outliers start: 13 outliers final: 12 residues processed: 103 average time/residue: 0.2895 time to fit residues: 38.8757 Evaluate side-chains 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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 27 LEU 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: 3.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.137801 restraints weight = 27345.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.141715 restraints weight = 12685.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.144167 restraints weight = 7299.670| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4525 Z= 0.186 Angle : 0.647 5.988 6185 Z= 0.327 Chirality : 0.053 0.330 700 Planarity : 0.007 0.046 795 Dihedral : 6.173 28.076 725 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.89 % Allowed : 16.29 % Favored : 80.82 % 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: -4.15 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 90 PHE 0.016 0.002 PHE C 86 TYR 0.011 0.002 TYR A 26 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 5) link_NAG-ASN : angle 2.94220 ( 15) hydrogen bonds : bond 0.03055 ( 77) hydrogen bonds : angle 4.92875 ( 216) SS BOND : bond 0.00423 ( 5) SS BOND : angle 0.57155 ( 10) covalent geometry : bond 0.00404 ( 4515) covalent geometry : angle 0.63108 ( 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 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.616 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: 0.6918 (pm20) cc_final: 0.6304 (pp30) REVERT: A 65 ASN cc_start: 0.2403 (OUTLIER) cc_final: 0.2022 (m110) REVERT: D 16 GLN cc_start: 0.7229 (pm20) cc_final: 0.6430 (pp30) REVERT: D 52 LYS cc_start: 0.6554 (tttt) cc_final: 0.4741 (pttm) REVERT: D 82 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7738 (mm-30) REVERT: E 82 GLU cc_start: 0.7266 (mm-30) cc_final: 0.5964 (pt0) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.2823 time to fit residues: 37.8813 Evaluate side-chains 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 61 PHE 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 27 LEU 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: 8.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4677 r_free = 0.4677 target = 0.160367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.143873 restraints weight = 26350.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.147579 restraints weight = 12432.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.149843 restraints weight = 7308.492| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4525 Z= 0.131 Angle : 0.587 4.729 6185 Z= 0.295 Chirality : 0.052 0.312 700 Planarity : 0.006 0.046 795 Dihedral : 5.731 23.464 725 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.47 % Allowed : 17.32 % Favored : 80.21 % 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: -4.11 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 90 PHE 0.014 0.001 PHE A 61 TYR 0.014 0.001 TYR A 26 ARG 0.001 0.000 ARG A 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 5) link_NAG-ASN : angle 2.93393 ( 15) hydrogen bonds : bond 0.02714 ( 77) hydrogen bonds : angle 4.84429 ( 216) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.25493 ( 10) covalent geometry : bond 0.00295 ( 4515) covalent geometry : angle 0.56772 ( 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 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.685 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: 0.6872 (pm20) cc_final: 0.6519 (pp30) REVERT: A 65 ASN cc_start: 0.2353 (OUTLIER) cc_final: 0.1963 (m110) REVERT: D 16 GLN cc_start: 0.7224 (pm20) cc_final: 0.6375 (pp30) REVERT: D 52 LYS cc_start: 0.6712 (tttt) cc_final: 0.4910 (pttm) REVERT: E 82 GLU cc_start: 0.7206 (mm-30) cc_final: 0.5997 (pt0) outliers start: 12 outliers final: 11 residues processed: 99 average time/residue: 0.2956 time to fit residues: 38.6510 Evaluate side-chains 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 61 PHE 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: 4.9990 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.159230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.142229 restraints weight = 26761.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.145860 restraints weight = 13246.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.148209 restraints weight = 8164.797| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.4476 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= 0.143 Angle : 0.592 4.727 6185 Z= 0.298 Chirality : 0.052 0.299 700 Planarity : 0.006 0.046 795 Dihedral : 5.808 24.912 725 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.89 % Allowed : 16.70 % Favored : 80.41 % 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: -4.17 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 90 PHE 0.014 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 0.00178 ( 5) link_NAG-ASN : angle 2.67559 ( 15) hydrogen bonds : bond 0.02702 ( 77) hydrogen bonds : angle 4.84079 ( 216) SS BOND : bond 0.00284 ( 5) SS BOND : angle 1.19940 ( 10) covalent geometry : bond 0.00320 ( 4515) covalent geometry : angle 0.57654 ( 6160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3459.24 seconds wall clock time: 60 minutes 46.54 seconds (3646.54 seconds total)