Starting phenix.real_space_refine on Wed Jan 15 17:43:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fac_50272/01_2025/9fac_50272_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fac_50272/01_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_50272/01_2025/9fac_50272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fac_50272/01_2025/9fac_50272.map" model { file = "/net/cci-nas-00/data/ceres_data/9fac_50272/01_2025/9fac_50272_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fac_50272/01_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-5571/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: 5.33, per 1000 atoms: 0.62 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: 2.21 Conformation dependent library (CDL) restraints added in 878.9 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: 0.84 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: 3.05 Time building geometry restraints manager: 2.69 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: 0.05 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 23.330 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 4515 Z= 0.473 Angle : 1.171 8.255 6160 Z= 0.652 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 *********************** 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 : 0.573 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: 52.9795 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 : 0.709 ------------------------------------------------------------------------------- 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 4515 Z= 0.204 Angle : 0.684 5.480 6160 Z= 0.360 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 *********************** 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 : 0.655 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: 0.2915 time to fit residues: 40.1270 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 : 0.631 ------------------------------------------------------------------------------- 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 4515 Z= 0.189 Angle : 0.606 5.385 6160 Z= 0.314 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 *********************** 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 : 0.618 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: 0.2901 time to fit residues: 39.4387 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 : 0.644 ------------------------------------------------------------------------------- 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: 0.6980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4703 r_free = 0.4703 target = 0.161720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.145297 restraints weight = 26039.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.149134 restraints weight = 12136.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.151381 restraints weight = 7016.691| |-----------------------------------------------------------------------------| r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4515 Z= 0.174 Angle : 0.565 5.413 6160 Z= 0.291 Chirality : 0.051 0.292 700 Planarity : 0.006 0.046 795 Dihedral : 5.560 19.671 725 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 0.006 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 *********************** 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 : 0.633 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: A 16 GLN cc_start: 0.6757 (pm20) cc_final: 0.6476 (pp30) REVERT: A 38 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7832 (ptpp) REVERT: A 65 ASN cc_start: 0.2405 (OUTLIER) cc_final: 0.2111 (m110) REVERT: B 82 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6972 (mm-30) REVERT: D 16 GLN cc_start: 0.6897 (pm20) cc_final: 0.6438 (pp30) REVERT: D 52 LYS cc_start: 0.6484 (tttt) cc_final: 0.4731 (pttm) REVERT: E 75 SER cc_start: 0.7806 (t) cc_final: 0.7602 (m) REVERT: E 82 GLU cc_start: 0.7218 (mm-30) cc_final: 0.5992 (pp20) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.2946 time to fit residues: 39.4644 Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.158715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.142396 restraints weight = 26438.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.146107 restraints weight = 12542.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.148378 restraints weight = 7338.822| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4515 Z= 0.258 Angle : 0.623 5.716 6160 Z= 0.322 Chirality : 0.052 0.308 700 Planarity : 0.007 0.046 795 Dihedral : 6.075 26.991 725 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.89 % Allowed : 14.64 % 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: -3.83 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 90 PHE 0.013 0.002 PHE B 61 TYR 0.008 0.002 TYR B 35 ARG 0.002 0.001 ARG A 53 *********************** 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 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6768 (pm20) cc_final: 0.6440 (pp30) REVERT: A 38 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7867 (ptpp) REVERT: A 65 ASN cc_start: 0.2675 (OUTLIER) cc_final: 0.2335 (m110) REVERT: D 16 GLN cc_start: 0.6977 (pm20) cc_final: 0.6236 (pp30) REVERT: D 52 LYS cc_start: 0.6552 (tttt) cc_final: 0.4809 (pttm) REVERT: E 75 SER cc_start: 0.8034 (t) cc_final: 0.7807 (m) REVERT: E 82 GLU cc_start: 0.7219 (mm-30) cc_final: 0.5940 (pt0) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.2665 time to fit residues: 36.6379 Evaluate side-chains 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.161581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.144716 restraints weight = 25937.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.148542 restraints weight = 12479.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.150865 restraints weight = 7311.309| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4515 Z= 0.151 Angle : 0.532 4.528 6160 Z= 0.272 Chirality : 0.051 0.286 700 Planarity : 0.006 0.043 795 Dihedral : 5.424 20.027 725 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.06 % Allowed : 15.67 % 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: -3.69 (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 0.003 0.001 TRP D 34 PHE 0.011 0.001 PHE B 61 TYR 0.010 0.001 TYR A 26 ARG 0.001 0.000 ARG E 32 *********************** 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: 10 poor density : 91 time to evaluate : 0.639 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: 0.6706 (pm20) cc_final: 0.6396 (pp30) REVERT: A 65 ASN cc_start: 0.2212 (OUTLIER) cc_final: 0.1945 (m110) REVERT: B 82 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7084 (mt-10) REVERT: D 16 GLN cc_start: 0.6928 (pm20) cc_final: 0.6276 (pp30) REVERT: D 52 LYS cc_start: 0.6546 (tttt) cc_final: 0.4799 (pttm) REVERT: E 75 SER cc_start: 0.7919 (t) cc_final: 0.7710 (m) REVERT: E 82 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6030 (pp20) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.2964 time to fit residues: 38.1092 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 : 0.617 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** E 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.161327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.144257 restraints weight = 26025.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.147943 restraints weight = 12693.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.150276 restraints weight = 7635.708| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4515 Z= 0.190 Angle : 0.550 4.763 6160 Z= 0.279 Chirality : 0.051 0.280 700 Planarity : 0.006 0.043 795 Dihedral : 5.512 22.154 725 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.27 % Allowed : 16.08 % Favored : 81.65 % 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: -3.74 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 PHE 0.012 0.001 PHE E 61 TYR 0.010 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 *********************** 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 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.658 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: 0.6731 (pm20) cc_final: 0.6367 (pp30) REVERT: A 65 ASN cc_start: 0.2249 (OUTLIER) cc_final: 0.1952 (m110) REVERT: C 16 GLN cc_start: 0.6854 (pp30) cc_final: 0.6513 (pp30) REVERT: D 16 GLN cc_start: 0.6957 (pm20) cc_final: 0.6375 (pp30) REVERT: D 52 LYS cc_start: 0.6654 (tttt) cc_final: 0.4884 (pttm) REVERT: E 75 SER cc_start: 0.8007 (t) cc_final: 0.7783 (m) REVERT: E 82 GLU cc_start: 0.7224 (mm-30) cc_final: 0.5968 (pt0) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2881 time to fit residues: 37.6567 Evaluate side-chains 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 0.0040 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 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 = 0.4678 r_free = 0.4678 target = 0.159835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.143174 restraints weight = 26215.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.146945 restraints weight = 12349.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.149280 restraints weight = 7281.569| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4515 Z= 0.199 Angle : 0.556 4.785 6160 Z= 0.283 Chirality : 0.051 0.287 700 Planarity : 0.006 0.044 795 Dihedral : 5.635 23.972 725 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.27 % Allowed : 16.08 % Favored : 81.65 % 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: -3.83 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 PHE 0.015 0.001 PHE E 61 TYR 0.013 0.001 TYR A 26 ARG 0.002 0.000 ARG A 53 *********************** 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 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 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: 0.6854 (pm20) cc_final: 0.6481 (pp30) REVERT: A 65 ASN cc_start: 0.2130 (OUTLIER) cc_final: 0.1784 (m110) REVERT: D 16 GLN cc_start: 0.7197 (pm20) cc_final: 0.6374 (pp30) REVERT: D 52 LYS cc_start: 0.6659 (tttt) cc_final: 0.4892 (pttm) REVERT: E 75 SER cc_start: 0.8105 (t) cc_final: 0.7826 (m) REVERT: E 82 GLU cc_start: 0.7225 (mm-30) cc_final: 0.5969 (pt0) outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.2878 time to fit residues: 37.0556 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 : 0.649 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 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 = 0.4700 r_free = 0.4700 target = 0.162917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.146415 restraints weight = 26270.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.150206 restraints weight = 12349.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.152587 restraints weight = 7196.400| |-----------------------------------------------------------------------------| r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4515 Z= 0.190 Angle : 0.546 4.691 6160 Z= 0.277 Chirality : 0.051 0.282 700 Planarity : 0.006 0.043 795 Dihedral : 5.483 22.750 725 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.47 % Allowed : 16.70 % 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: -3.90 (0.25), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 90 PHE 0.011 0.001 PHE E 61 TYR 0.013 0.001 TYR A 26 ARG 0.001 0.000 ARG A 53 *********************** 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 106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.704 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: 0.6856 (pm20) cc_final: 0.6467 (pp30) REVERT: A 65 ASN cc_start: 0.2139 (OUTLIER) cc_final: 0.1776 (m110) REVERT: D 16 GLN cc_start: 0.7177 (pm20) cc_final: 0.6370 (pp30) REVERT: D 52 LYS cc_start: 0.6808 (tttt) cc_final: 0.4979 (pttm) REVERT: E 75 SER cc_start: 0.8144 (t) cc_final: 0.7844 (m) REVERT: E 82 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6021 (pt0) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.2919 time to fit residues: 38.8571 Evaluate side-chains 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4671 r_free = 0.4671 target = 0.159747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.143610 restraints weight = 26582.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.147302 restraints weight = 12726.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.149710 restraints weight = 7399.516| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4515 Z= 0.275 Angle : 0.620 5.825 6160 Z= 0.318 Chirality : 0.052 0.310 700 Planarity : 0.007 0.045 795 Dihedral : 6.193 28.956 725 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % 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: -4.18 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 90 PHE 0.014 0.002 PHE E 61 TYR 0.012 0.002 TYR A 26 ARG 0.001 0.000 ARG A 53 ********************** 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 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.694 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: 0.6932 (pm20) cc_final: 0.6496 (pp30) REVERT: A 65 ASN cc_start: 0.2369 (OUTLIER) cc_final: 0.1969 (m110) REVERT: B 65 ASN cc_start: 0.1509 (OUTLIER) cc_final: 0.0942 (m110) REVERT: D 16 GLN cc_start: 0.7308 (pm20) cc_final: 0.6576 (pp30) REVERT: D 52 LYS cc_start: 0.6726 (tttt) cc_final: 0.4923 (pttm) REVERT: E 75 SER cc_start: 0.8346 (t) cc_final: 0.8009 (m) REVERT: E 82 GLU cc_start: 0.7227 (mm-30) cc_final: 0.5949 (pt0) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.2910 time to fit residues: 38.9432 Evaluate side-chains 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 61 PHE Chi-restraints excluded: chain B 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 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: 5.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- 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 = 0.4666 r_free = 0.4666 target = 0.156750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.140197 restraints weight = 26687.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.143965 restraints weight = 12796.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.146332 restraints weight = 7488.167| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.277 4515 Z= 0.304 Angle : 1.138 59.198 6160 Z= 0.697 Chirality : 0.061 0.844 700 Planarity : 0.007 0.046 795 Dihedral : 6.175 28.908 725 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.17 % Favored : 91.65 % Rotamer: Outliers : 2.47 % Allowed : 17.32 % Favored : 80.21 % Cbeta Deviations : 0.19 % 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: -4.20 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 90 PHE 0.012 0.002 PHE E 61 TYR 0.010 0.002 TYR A 26 ARG 0.001 0.000 ARG A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.27 seconds wall clock time: 60 minutes 40.59 seconds (3640.59 seconds total)