Starting phenix.real_space_refine on Fri Nov 15 08:48:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fac_50272/11_2024/9fac_50272_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fac_50272/11_2024/9fac_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fac_50272/11_2024/9fac_50272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fac_50272/11_2024/9fac_50272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fac_50272/11_2024/9fac_50272_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fac_50272/11_2024/9fac_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-5513/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: 5.11, 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: 2.10 Conformation dependent library (CDL) restraints added in 969.2 milliseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 13 sheets defined 4.3% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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: 2.92 Time building geometry restraints manager: 2.52 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: 0.00 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: 1.620 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.440 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- 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 : 0.606 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: 0.3170 time to fit residues: 53.6998 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 : 0.715 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 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 : 0.698 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: 0.6532 (pm20) cc_final: 0.6156 (pp30) REVERT: B 16 GLN cc_start: 0.5898 (pm20) cc_final: 0.5568 (pp30) REVERT: B 78 GLN cc_start: 0.8025 (tt0) cc_final: 0.7558 (tt0) REVERT: C 77 THR cc_start: 0.7538 (p) cc_final: 0.7278 (m) REVERT: D 16 GLN cc_start: 0.6683 (pm20) cc_final: 0.6114 (pp30) REVERT: D 52 LYS cc_start: 0.6093 (tttt) cc_final: 0.4514 (pttm) REVERT: E 52 LYS cc_start: 0.5879 (tttt) cc_final: 0.5549 (mtpt) REVERT: E 75 SER cc_start: 0.7339 (t) cc_final: 0.7081 (m) REVERT: E 82 GLU cc_start: 0.7285 (mm-30) cc_final: 0.5857 (pp20) REVERT: E 93 THR cc_start: 0.8358 (m) cc_final: 0.8030 (p) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2917 time to fit residues: 40.1746 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 : 0.814 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4515 Z= 0.320 Angle : 0.740 6.769 6160 Z= 0.388 Chirality : 0.056 0.348 700 Planarity : 0.007 0.047 795 Dihedral : 6.999 30.977 725 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.47 % Allowed : 14.02 % Favored : 83.51 % 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: -4.09 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 90 PHE 0.015 0.002 PHE C 86 TYR 0.010 0.002 TYR B 35 ARG 0.003 0.001 ARG E 53 *********************** 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 111 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.693 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: 0.6629 (pm20) cc_final: 0.6182 (pp30) REVERT: A 38 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8052 (ptpp) REVERT: A 65 ASN cc_start: 0.3171 (OUTLIER) cc_final: 0.2809 (m110) REVERT: A 80 LEU cc_start: 0.8264 (mp) cc_final: 0.8000 (mp) REVERT: B 16 GLN cc_start: 0.6214 (pm20) cc_final: 0.5701 (pp30) REVERT: D 16 GLN cc_start: 0.6802 (pm20) cc_final: 0.6140 (pp30) REVERT: D 52 LYS cc_start: 0.6306 (tttt) cc_final: 0.4526 (pttm) REVERT: E 75 SER cc_start: 0.7849 (t) cc_final: 0.7501 (m) REVERT: E 93 THR cc_start: 0.8465 (m) cc_final: 0.8217 (p) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.2944 time to fit residues: 40.7317 Evaluate side-chains 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 27 LEU 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 57 ILE 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 49 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN C 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4515 Z= 0.297 Angle : 0.691 6.075 6160 Z= 0.362 Chirality : 0.055 0.346 700 Planarity : 0.007 0.046 795 Dihedral : 6.722 27.601 725 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.51 % Allowed : 15.46 % Favored : 81.03 % 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: -4.24 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 90 PHE 0.011 0.002 PHE C 86 TYR 0.010 0.002 TYR D 35 ARG 0.003 0.001 ARG A 53 *********************** 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 114 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.684 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: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6762 (pm20) cc_final: 0.6257 (pp30) REVERT: A 38 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8009 (ptpp) REVERT: A 65 ASN cc_start: 0.2852 (OUTLIER) cc_final: 0.2496 (m110) REVERT: B 16 GLN cc_start: 0.6308 (pm20) cc_final: 0.5729 (pp30) REVERT: D 16 GLN cc_start: 0.6967 (pm20) cc_final: 0.6090 (pp30) REVERT: D 52 LYS cc_start: 0.6336 (tttt) cc_final: 0.4517 (pttm) REVERT: E 75 SER cc_start: 0.8065 (t) cc_final: 0.7691 (m) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.2761 time to fit residues: 40.0570 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 : 0.711 ------------------------------------------------------------------------------- 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 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 22 CYS Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 16 GLN 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 44 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4515 Z= 0.187 Angle : 0.605 5.466 6160 Z= 0.313 Chirality : 0.053 0.316 700 Planarity : 0.007 0.045 795 Dihedral : 6.170 23.642 725 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.27 % Allowed : 17.11 % Favored : 80.62 % 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: -4.14 (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 0.004 0.001 TRP D 34 PHE 0.011 0.001 PHE A 61 TYR 0.009 0.001 TYR A 26 ARG 0.001 0.000 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 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6696 (pm20) cc_final: 0.6239 (pp30) REVERT: A 38 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7974 (ptpp) REVERT: A 65 ASN cc_start: 0.2730 (OUTLIER) cc_final: 0.2396 (m110) REVERT: B 16 GLN cc_start: 0.6225 (pm20) cc_final: 0.5682 (pp30) REVERT: D 16 GLN cc_start: 0.6994 (pm20) cc_final: 0.6144 (pp30) REVERT: D 52 LYS cc_start: 0.6354 (tttt) cc_final: 0.4547 (pttm) REVERT: E 75 SER cc_start: 0.8003 (t) cc_final: 0.7640 (m) REVERT: E 82 GLU cc_start: 0.7178 (mm-30) cc_final: 0.5885 (pt0) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.2852 time to fit residues: 38.0325 Evaluate side-chains 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 16 GLN 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 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4515 Z= 0.315 Angle : 0.683 6.081 6160 Z= 0.353 Chirality : 0.053 0.321 700 Planarity : 0.007 0.047 795 Dihedral : 6.852 31.806 725 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.30 % Allowed : 17.32 % Favored : 79.38 % 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: -4.28 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 90 PHE 0.015 0.002 PHE B 61 TYR 0.011 0.002 TYR B 35 ARG 0.003 0.001 ARG A 53 *********************** 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 113 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.319 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: 0.6832 (pm20) cc_final: 0.6292 (pp30) REVERT: A 38 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7994 (ptpp) REVERT: A 65 ASN cc_start: 0.2814 (OUTLIER) cc_final: 0.2429 (m110) REVERT: B 16 GLN cc_start: 0.6354 (pm20) cc_final: 0.5668 (pp30) REVERT: D 16 GLN cc_start: 0.7140 (pm20) cc_final: 0.6140 (pp30) REVERT: D 52 LYS cc_start: 0.6402 (tttt) cc_final: 0.4563 (pttm) REVERT: E 75 SER cc_start: 0.8129 (t) cc_final: 0.7739 (m) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.2979 time to fit residues: 42.8127 Evaluate side-chains 110 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 22 CYS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 16 GLN 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 5 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 overall best weight: 1.0840 ------------------------------------------------------------------------------- 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** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.4199 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= 0.201 Angle : 0.601 5.414 6160 Z= 0.309 Chirality : 0.052 0.313 700 Planarity : 0.007 0.046 795 Dihedral : 6.164 24.814 725 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.30 % Allowed : 17.94 % Favored : 78.76 % 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: -4.24 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 90 PHE 0.011 0.001 PHE B 61 TYR 0.010 0.001 TYR A 26 ARG 0.001 0.000 ARG B 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 113 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6798 (pm20) cc_final: 0.6306 (pp30) REVERT: A 65 ASN cc_start: 0.2531 (OUTLIER) cc_final: 0.2175 (m110) REVERT: B 16 GLN cc_start: 0.6412 (pm20) cc_final: 0.5612 (pp30) REVERT: D 16 GLN cc_start: 0.7102 (pm20) cc_final: 0.6119 (pp30) REVERT: D 52 LYS cc_start: 0.6381 (tttt) cc_final: 0.4587 (pttm) REVERT: E 75 SER cc_start: 0.8178 (t) cc_final: 0.7770 (m) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.2995 time to fit residues: 42.1816 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 : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 17 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 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4515 Z= 0.185 Angle : 0.565 5.433 6160 Z= 0.289 Chirality : 0.051 0.276 700 Planarity : 0.007 0.044 795 Dihedral : 5.773 23.607 725 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.09 % Allowed : 17.53 % Favored : 79.38 % 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 0.010 0.001 TRP B 90 PHE 0.012 0.001 PHE B 61 TYR 0.013 0.001 TYR A 26 ARG 0.001 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 112 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.712 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: 0.6767 (pm20) cc_final: 0.6269 (pp30) REVERT: A 65 ASN cc_start: 0.2311 (OUTLIER) cc_final: 0.1935 (m110) REVERT: B 16 GLN cc_start: 0.6399 (pm20) cc_final: 0.5585 (pp30) REVERT: D 16 GLN cc_start: 0.7118 (pm20) cc_final: 0.6138 (pp30) REVERT: D 52 LYS cc_start: 0.6432 (tttt) cc_final: 0.4593 (pttm) REVERT: E 75 SER cc_start: 0.8157 (t) cc_final: 0.7745 (m) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.2625 time to fit residues: 37.1613 Evaluate side-chains 111 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE 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 50 SER 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 65 ASN 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 50 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4515 Z= 0.259 Angle : 0.620 5.591 6160 Z= 0.318 Chirality : 0.052 0.296 700 Planarity : 0.007 0.044 795 Dihedral : 6.381 30.362 725 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.12 % Allowed : 17.11 % Favored : 78.76 % 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: -4.39 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 90 PHE 0.009 0.001 PHE C 86 TYR 0.011 0.002 TYR A 26 ARG 0.002 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 114 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.700 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: 0.6828 (pm20) cc_final: 0.6262 (pp30) REVERT: A 65 ASN cc_start: 0.2544 (OUTLIER) cc_final: 0.2110 (m110) REVERT: B 16 GLN cc_start: 0.6449 (pm20) cc_final: 0.5577 (pp30) REVERT: B 65 ASN cc_start: 0.1603 (OUTLIER) cc_final: 0.1068 (m110) REVERT: D 16 GLN cc_start: 0.7162 (pm20) cc_final: 0.6067 (pp30) REVERT: D 52 LYS cc_start: 0.6454 (tttt) cc_final: 0.4622 (pttm) REVERT: E 75 SER cc_start: 0.8279 (t) cc_final: 0.7896 (m) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.2687 time to fit residues: 38.7119 Evaluate side-chains 108 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 GLN 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 50 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 65 ASN 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 24 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 4515 Z= 0.263 Angle : 1.131 59.188 6160 Z= 0.676 Chirality : 0.053 0.291 700 Planarity : 0.007 0.045 795 Dihedral : 6.356 30.249 725 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.68 % Allowed : 17.53 % Favored : 79.79 % 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: -4.40 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 90 PHE 0.009 0.001 PHE B 61 TYR 0.010 0.001 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 106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.696 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: 0.6855 (pm20) cc_final: 0.6295 (pp30) REVERT: A 65 ASN cc_start: 0.2520 (OUTLIER) cc_final: 0.2097 (m110) REVERT: B 16 GLN cc_start: 0.6440 (pm20) cc_final: 0.5583 (pp30) REVERT: D 16 GLN cc_start: 0.7149 (pm20) cc_final: 0.6064 (pp30) REVERT: D 52 LYS cc_start: 0.6449 (tttt) cc_final: 0.4620 (pttm) REVERT: E 75 SER cc_start: 0.8273 (t) cc_final: 0.7893 (m) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 0.2666 time to fit residues: 35.7934 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 65 ASN 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 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.4632 r_free = 0.4632 target = 0.155265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.139911 restraints weight = 27053.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.143465 restraints weight = 12616.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.145613 restraints weight = 7318.587| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 4515 Z= 0.263 Angle : 1.131 59.200 6160 Z= 0.676 Chirality : 0.053 0.291 700 Planarity : 0.007 0.045 795 Dihedral : 6.356 30.249 725 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.68 % Allowed : 17.53 % Favored : 79.79 % 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: -4.40 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 90 PHE 0.009 0.001 PHE B 61 TYR 0.010 0.001 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: 2903.18 seconds wall clock time: 52 minutes 32.40 seconds (3152.40 seconds total)