Starting phenix.real_space_refine on Sat Mar 16 20:58:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/03_2024/6zgl_11210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/03_2024/6zgl_11210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/03_2024/6zgl_11210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/03_2024/6zgl_11210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/03_2024/6zgl_11210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/03_2024/6zgl_11210.pdb" } resolution = 1.9 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= 0.003 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 9324 2.51 5 N 2568 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15760 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "C" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "E" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "F" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "G" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "H" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "I" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "J" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "K" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "L" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "J" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "K" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "L" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Time building chain proxies: 15.78, per 1000 atoms: 1.00 Number of scatterers: 15760 At special positions: 0 Unit cell: (105.298, 101.422, 94.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3832 8.00 N 2568 7.00 C 9324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 5.0 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 22 through 54 Processing helix chain 'A' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 Processing helix chain 'B' and resid 22 through 54 Processing helix chain 'B' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 67 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 Processing helix chain 'C' and resid 22 through 54 Processing helix chain 'C' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 67 " --> pdb=" O HIS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 165 Processing helix chain 'D' and resid 22 through 54 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 67 " --> pdb=" O HIS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 113 through 139 removed outlier: 4.272A pdb=" N GLY D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 165 Processing helix chain 'E' and resid 22 through 54 Processing helix chain 'E' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 67 " --> pdb=" O HIS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 Processing helix chain 'E' and resid 113 through 139 removed outlier: 4.272A pdb=" N GLY E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 165 Processing helix chain 'F' and resid 22 through 54 Processing helix chain 'F' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP F 67 " --> pdb=" O HIS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 102 Processing helix chain 'F' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 165 Processing helix chain 'G' and resid 22 through 54 Processing helix chain 'G' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 67 " --> pdb=" O HIS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 102 Processing helix chain 'G' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 165 Processing helix chain 'H' and resid 22 through 54 Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 102 Processing helix chain 'H' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY H 137 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 165 Processing helix chain 'I' and resid 22 through 54 Processing helix chain 'I' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL I 62 " --> pdb=" O ASN I 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP I 67 " --> pdb=" O HIS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'I' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY I 137 " --> pdb=" O ARG I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 165 Processing helix chain 'J' and resid 22 through 54 Processing helix chain 'J' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL J 62 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP J 67 " --> pdb=" O HIS J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 102 Processing helix chain 'J' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 165 Processing helix chain 'K' and resid 22 through 54 Processing helix chain 'K' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL K 62 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP K 67 " --> pdb=" O HIS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 102 Processing helix chain 'K' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY K 137 " --> pdb=" O ARG K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 165 Processing helix chain 'L' and resid 22 through 54 Processing helix chain 'L' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL L 62 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP L 67 " --> pdb=" O HIS L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 102 Processing helix chain 'L' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY L 137 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 165 1212 hydrogen bonds defined for protein. 3612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 7.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3925 1.33 - 1.46: 3738 1.46 - 1.59: 7301 1.59 - 1.72: 0 1.72 - 1.85: 72 Bond restraints: 15036 Sorted by residual: bond pdb=" C GLU G 31 " pdb=" CA BGLU G 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.76e+01 bond pdb=" C GLU E 31 " pdb=" CA BGLU E 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.75e+01 bond pdb=" C GLU J 31 " pdb=" CA BGLU J 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.75e+01 bond pdb=" C GLU I 31 " pdb=" CA BGLU I 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.74e+01 bond pdb=" C GLU F 31 " pdb=" CA BGLU F 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.74e+01 ... (remaining 15031 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.79: 120 104.79 - 112.08: 7151 112.08 - 119.37: 6164 119.37 - 126.66: 6809 126.66 - 133.95: 156 Bond angle restraints: 20400 Sorted by residual: angle pdb=" CA SER D 100 " pdb=" C SER D 100 " pdb=" O SER D 100 " ideal model delta sigma weight residual 119.79 128.17 -8.38 1.18e+00 7.18e-01 5.04e+01 angle pdb=" CA SER E 100 " pdb=" C SER E 100 " pdb=" O SER E 100 " ideal model delta sigma weight residual 119.79 128.14 -8.35 1.18e+00 7.18e-01 5.01e+01 angle pdb=" CA SER J 100 " pdb=" C SER J 100 " pdb=" O SER J 100 " ideal model delta sigma weight residual 119.79 128.13 -8.34 1.18e+00 7.18e-01 4.99e+01 angle pdb=" CA SER H 100 " pdb=" C SER H 100 " pdb=" O SER H 100 " ideal model delta sigma weight residual 119.79 128.13 -8.34 1.18e+00 7.18e-01 4.99e+01 angle pdb=" CA SER F 100 " pdb=" C SER F 100 " pdb=" O SER F 100 " ideal model delta sigma weight residual 119.79 128.13 -8.34 1.18e+00 7.18e-01 4.99e+01 ... (remaining 20395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 7995 17.43 - 34.87: 981 34.87 - 52.30: 144 52.30 - 69.74: 60 69.74 - 87.17: 12 Dihedral angle restraints: 9192 sinusoidal: 3672 harmonic: 5520 Sorted by residual: dihedral pdb=" C THR B 29 " pdb=" N THR B 29 " pdb=" CA THR B 29 " pdb=" CB THR B 29 " ideal model delta harmonic sigma weight residual -122.00 -131.91 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C THR E 29 " pdb=" N THR E 29 " pdb=" CA THR E 29 " pdb=" CB THR E 29 " ideal model delta harmonic sigma weight residual -122.00 -131.90 9.90 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C THR D 29 " pdb=" N THR D 29 " pdb=" CA THR D 29 " pdb=" CB THR D 29 " ideal model delta harmonic sigma weight residual -122.00 -131.90 9.90 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 9189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1762 0.107 - 0.213: 519 0.213 - 0.319: 71 0.319 - 0.426: 28 0.426 - 0.532: 20 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CG LEU D 66 " pdb=" CB LEU D 66 " pdb=" CD1 LEU D 66 " pdb=" CD2 LEU D 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CG LEU B 66 " pdb=" CB LEU B 66 " pdb=" CD1 LEU B 66 " pdb=" CD2 LEU B 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CG LEU K 66 " pdb=" CB LEU K 66 " pdb=" CD1 LEU K 66 " pdb=" CD2 LEU K 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.08e+00 ... (remaining 2397 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 59 " 0.018 2.00e-02 2.50e+03 4.43e-02 3.43e+01 pdb=" CG PHE F 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE F 59 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE F 59 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE F 59 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE F 59 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE F 59 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 59 " 0.018 2.00e-02 2.50e+03 4.42e-02 3.42e+01 pdb=" CG PHE K 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 59 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE K 59 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE K 59 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE K 59 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE K 59 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 59 " -0.018 2.00e-02 2.50e+03 4.42e-02 3.42e+01 pdb=" CG PHE B 59 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 59 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE B 59 " -0.081 2.00e-02 2.50e+03 pdb=" CZ PHE B 59 " 0.056 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1998 2.74 - 3.28: 18358 3.28 - 3.82: 31261 3.82 - 4.36: 38557 4.36 - 4.90: 62168 Nonbonded interactions: 152342 Sorted by model distance: nonbonded pdb=" OD1 ASP E 75 " pdb=" O HOH E 201 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASP I 75 " pdb=" O HOH I 201 " model vdw 2.197 2.440 nonbonded pdb=" OD1 ASP H 75 " pdb=" O HOH H 201 " model vdw 2.201 2.440 nonbonded pdb=" OD1 ASP J 75 " pdb=" O HOH J 201 " model vdw 2.202 2.440 nonbonded pdb=" OD1 ASP L 75 " pdb=" O HOH L 201 " model vdw 2.204 2.440 ... (remaining 152337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'B' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'C' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'D' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'E' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'F' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'G' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'H' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'I' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'J' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'K' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'L' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.010 Extract box with map and model: 6.410 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 53.620 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.013 0.067 15036 Z= 0.845 Angle : 1.549 8.379 20400 Z= 1.068 Chirality : 0.115 0.532 2400 Planarity : 0.010 0.044 2640 Dihedral : 15.524 87.169 5592 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.73 % Allowed : 8.21 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 1848 helix: 0.45 (0.12), residues: 1404 sheet: None (None), residues: 0 loop : -0.77 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.013 TRP I 160 HIS 0.010 0.003 HIS G 51 PHE 0.081 0.012 PHE F 59 TYR 0.036 0.014 TYR J 16 ARG 0.031 0.005 ARG L 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 275 time to evaluate : 1.942 Fit side-chains REVERT: A 25 GLU cc_start: 0.6760 (tt0) cc_final: 0.6329 (tp30) REVERT: A 134 LYS cc_start: 0.7747 (mttp) cc_final: 0.7534 (mttt) REVERT: B 25 GLU cc_start: 0.6780 (tt0) cc_final: 0.6328 (tp30) REVERT: B 142 ASP cc_start: 0.7973 (m-30) cc_final: 0.7734 (m-30) REVERT: C 25 GLU cc_start: 0.6764 (tt0) cc_final: 0.6331 (tp30) REVERT: C 101 LYS cc_start: 0.7221 (mttt) cc_final: 0.6932 (mttm) REVERT: D 101 LYS cc_start: 0.7262 (mttt) cc_final: 0.7023 (mttm) REVERT: D 134 LYS cc_start: 0.7748 (mttp) cc_final: 0.7537 (mttp) REVERT: D 138 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: E 22 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (p) REVERT: E 25 GLU cc_start: 0.6758 (tt0) cc_final: 0.6317 (tp30) REVERT: E 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7486 (mttp) REVERT: F 25 GLU cc_start: 0.6737 (tt0) cc_final: 0.6352 (tp30) REVERT: F 70 ARG cc_start: 0.8416 (ttt180) cc_final: 0.7465 (ttp80) REVERT: F 75 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (t70) REVERT: F 101 LYS cc_start: 0.7181 (mttt) cc_final: 0.6896 (mttm) REVERT: F 134 LYS cc_start: 0.7664 (mttp) cc_final: 0.7463 (mttt) REVERT: G 25 GLU cc_start: 0.6671 (tt0) cc_final: 0.6261 (tp30) REVERT: G 35 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7730 (mtm110) REVERT: G 134 LYS cc_start: 0.7695 (mttp) cc_final: 0.7478 (mttm) REVERT: H 24 SER cc_start: 0.7174 (OUTLIER) cc_final: 0.6967 (p) REVERT: H 25 GLU cc_start: 0.6767 (tt0) cc_final: 0.6349 (tp30) REVERT: H 70 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8116 (ttt180) REVERT: H 75 ASP cc_start: 0.8558 (m-30) cc_final: 0.8269 (t70) REVERT: H 120 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8180 (mm-30) REVERT: H 138 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: H 142 ASP cc_start: 0.7942 (m-30) cc_final: 0.7644 (m-30) REVERT: I 25 GLU cc_start: 0.6744 (tt0) cc_final: 0.6359 (tp30) REVERT: I 101 LYS cc_start: 0.7180 (mttt) cc_final: 0.6910 (mttm) REVERT: J 35 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: J 101 LYS cc_start: 0.7248 (mttt) cc_final: 0.7033 (mttm) REVERT: J 134 LYS cc_start: 0.7731 (mttp) cc_final: 0.7489 (mttp) REVERT: J 142 ASP cc_start: 0.8001 (m-30) cc_final: 0.7790 (m-30) REVERT: K 25 GLU cc_start: 0.6860 (tt0) cc_final: 0.6367 (tp30) REVERT: K 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7154 (mtpt) REVERT: K 142 ASP cc_start: 0.8026 (m-30) cc_final: 0.7781 (m-30) REVERT: L 25 GLU cc_start: 0.6769 (tt0) cc_final: 0.6321 (tp30) REVERT: L 101 LYS cc_start: 0.7307 (mttt) cc_final: 0.7052 (mttm) REVERT: L 142 ASP cc_start: 0.7957 (m-30) cc_final: 0.7726 (m-30) outliers start: 48 outliers final: 9 residues processed: 287 average time/residue: 1.8681 time to fit residues: 574.6353 Evaluate side-chains 288 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN D 113 ASN E 113 ASN F 113 ASN G 113 ASN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 15036 Z= 0.161 Angle : 0.520 6.326 20400 Z= 0.293 Chirality : 0.038 0.122 2400 Planarity : 0.003 0.017 2640 Dihedral : 4.439 31.592 2053 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.75 % Allowed : 9.02 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.18), residues: 1848 helix: 2.78 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.25 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 52 HIS 0.006 0.001 HIS B 63 PHE 0.011 0.002 PHE L 69 TYR 0.007 0.001 TYR C 16 ARG 0.003 0.001 ARG L 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.902 Fit side-chains REVERT: A 35 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7523 (ttp80) REVERT: A 70 ARG cc_start: 0.8395 (tpt170) cc_final: 0.7616 (ttp80) REVERT: A 134 LYS cc_start: 0.7600 (mttp) cc_final: 0.7072 (mtpt) REVERT: B 25 GLU cc_start: 0.6755 (tt0) cc_final: 0.6267 (tp30) REVERT: C 55 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7815 (ptm160) REVERT: E 134 LYS cc_start: 0.7652 (mttp) cc_final: 0.7397 (mttp) REVERT: F 25 GLU cc_start: 0.6708 (tt0) cc_final: 0.6255 (tp30) REVERT: F 70 ARG cc_start: 0.8401 (ttt180) cc_final: 0.7475 (ttp80) REVERT: F 134 LYS cc_start: 0.7618 (mttp) cc_final: 0.7070 (mtpt) REVERT: G 134 LYS cc_start: 0.7643 (mttp) cc_final: 0.7389 (mttp) REVERT: H 35 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7561 (ttp80) REVERT: H 134 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7141 (mtpt) REVERT: I 25 GLU cc_start: 0.6725 (tt0) cc_final: 0.6275 (tp30) REVERT: I 101 LYS cc_start: 0.7284 (mttt) cc_final: 0.6940 (mttm) REVERT: I 134 LYS cc_start: 0.7640 (mttp) cc_final: 0.7233 (mtpt) REVERT: J 25 GLU cc_start: 0.6935 (tt0) cc_final: 0.6546 (tp30) REVERT: J 35 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7485 (ttp80) REVERT: J 55 ARG cc_start: 0.8170 (ptp-110) cc_final: 0.7960 (ptm160) REVERT: J 101 LYS cc_start: 0.7228 (mttt) cc_final: 0.6941 (mttm) REVERT: J 134 LYS cc_start: 0.7680 (mttp) cc_final: 0.7092 (mtpt) REVERT: K 25 GLU cc_start: 0.6707 (tt0) cc_final: 0.6272 (tp30) REVERT: K 134 LYS cc_start: 0.7633 (mttp) cc_final: 0.7414 (mtmm) REVERT: L 35 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7432 (ttp80) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 1.8726 time to fit residues: 612.2587 Evaluate side-chains 286 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN G 113 ASN H 39 GLN H 113 ASN I 39 GLN I 113 ASN J 39 GLN J 113 ASN K 39 GLN L 113 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15036 Z= 0.233 Angle : 0.599 9.153 20400 Z= 0.343 Chirality : 0.042 0.158 2400 Planarity : 0.004 0.037 2640 Dihedral : 4.164 20.031 2028 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.18 % Allowed : 10.63 % Favored : 88.18 % 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: 3.11 (0.17), residues: 1848 helix: 2.51 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.45 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 52 HIS 0.008 0.002 HIS B 63 PHE 0.014 0.002 PHE C 59 TYR 0.011 0.002 TYR I 16 ARG 0.005 0.001 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 283 time to evaluate : 1.529 Fit side-chains REVERT: A 134 LYS cc_start: 0.7697 (mttp) cc_final: 0.7454 (mttt) REVERT: B 25 GLU cc_start: 0.6793 (tt0) cc_final: 0.6311 (tp30) REVERT: B 142 ASP cc_start: 0.7882 (m-30) cc_final: 0.7676 (m-30) REVERT: C 142 ASP cc_start: 0.7829 (m-30) cc_final: 0.7611 (m-30) REVERT: E 134 LYS cc_start: 0.7720 (mttp) cc_final: 0.7469 (mttp) REVERT: F 25 GLU cc_start: 0.6889 (tt0) cc_final: 0.6427 (tp30) REVERT: F 70 ARG cc_start: 0.8365 (ttt180) cc_final: 0.7575 (ttp80) REVERT: F 134 LYS cc_start: 0.7668 (mttp) cc_final: 0.7109 (mtpt) REVERT: G 134 LYS cc_start: 0.7701 (mttp) cc_final: 0.7456 (mttp) REVERT: H 25 GLU cc_start: 0.6972 (tt0) cc_final: 0.6531 (tp30) REVERT: I 25 GLU cc_start: 0.6870 (tt0) cc_final: 0.6416 (tp30) REVERT: I 134 LYS cc_start: 0.7826 (mttp) cc_final: 0.7333 (mtpt) REVERT: J 101 LYS cc_start: 0.7251 (mttt) cc_final: 0.6961 (mttm) REVERT: J 134 LYS cc_start: 0.7677 (mttp) cc_final: 0.7458 (mttp) REVERT: K 25 GLU cc_start: 0.6746 (tt0) cc_final: 0.6338 (tp30) outliers start: 7 outliers final: 4 residues processed: 284 average time/residue: 1.9604 time to fit residues: 595.0895 Evaluate side-chains 283 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 279 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN C 113 ASN D 113 ASN E 113 ASN F 39 GLN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN J 113 ASN K 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15036 Z= 0.191 Angle : 0.548 7.945 20400 Z= 0.311 Chirality : 0.040 0.142 2400 Planarity : 0.003 0.026 2640 Dihedral : 4.118 19.012 2028 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.12 % Allowed : 11.26 % Favored : 87.62 % 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: 3.31 (0.17), residues: 1848 helix: 2.60 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.68 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 52 HIS 0.006 0.002 HIS B 63 PHE 0.010 0.002 PHE C 59 TYR 0.008 0.001 TYR C 16 ARG 0.003 0.001 ARG L 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 287 time to evaluate : 1.899 Fit side-chains REVERT: A 134 LYS cc_start: 0.7658 (mttp) cc_final: 0.7410 (mttt) REVERT: C 70 ARG cc_start: 0.8356 (ttt180) cc_final: 0.7645 (ttp80) REVERT: C 142 ASP cc_start: 0.7764 (m-30) cc_final: 0.7547 (m-30) REVERT: D 55 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7529 (ptm160) REVERT: E 134 LYS cc_start: 0.7705 (mttp) cc_final: 0.7497 (mttm) REVERT: F 134 LYS cc_start: 0.7666 (mttp) cc_final: 0.7112 (mtpt) REVERT: H 25 GLU cc_start: 0.6919 (tt0) cc_final: 0.6487 (tp30) REVERT: I 25 GLU cc_start: 0.6853 (tt0) cc_final: 0.6392 (tp30) REVERT: I 134 LYS cc_start: 0.7789 (mttp) cc_final: 0.7314 (mtpt) REVERT: J 101 LYS cc_start: 0.7174 (mttt) cc_final: 0.6925 (mttm) outliers start: 6 outliers final: 5 residues processed: 287 average time/residue: 1.9397 time to fit residues: 596.2384 Evaluate side-chains 288 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 282 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain L residue 138 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 36 GLN F 39 GLN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN J 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15036 Z= 0.310 Angle : 0.671 8.248 20400 Z= 0.383 Chirality : 0.045 0.183 2400 Planarity : 0.005 0.053 2640 Dihedral : 4.417 20.407 2028 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.37 % Allowed : 10.57 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.17), residues: 1848 helix: 2.21 (0.12), residues: 1428 sheet: None (None), residues: 0 loop : 0.55 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 160 HIS 0.009 0.003 HIS B 63 PHE 0.014 0.003 PHE C 59 TYR 0.013 0.002 TYR C 16 ARG 0.010 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 1.908 Fit side-chains REVERT: A 55 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (ptm160) REVERT: A 134 LYS cc_start: 0.7730 (mttp) cc_final: 0.7511 (mttp) REVERT: B 25 GLU cc_start: 0.6932 (tt0) cc_final: 0.6470 (tp30) REVERT: C 70 ARG cc_start: 0.8346 (ttt180) cc_final: 0.7650 (ttp80) REVERT: C 142 ASP cc_start: 0.7894 (m-30) cc_final: 0.7636 (m-30) REVERT: D 55 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7741 (ptm160) REVERT: E 134 LYS cc_start: 0.7727 (mttp) cc_final: 0.7463 (mttp) REVERT: F 25 GLU cc_start: 0.6928 (tt0) cc_final: 0.6466 (tp30) REVERT: F 134 LYS cc_start: 0.7707 (mttp) cc_final: 0.7159 (mtpt) REVERT: G 55 ARG cc_start: 0.8270 (ptp90) cc_final: 0.7941 (ptm160) REVERT: H 25 GLU cc_start: 0.6988 (tt0) cc_final: 0.6540 (tp30) REVERT: I 25 GLU cc_start: 0.6956 (tt0) cc_final: 0.6501 (tp30) REVERT: I 134 LYS cc_start: 0.7809 (mttp) cc_final: 0.7337 (mtpt) REVERT: L 138 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6989 (mt-10) outliers start: 10 outliers final: 5 residues processed: 284 average time/residue: 1.9370 time to fit residues: 588.8550 Evaluate side-chains 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 281 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain L residue 138 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 0.4980 chunk 144 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN C 113 ASN D 113 ASN E 113 ASN F 39 GLN F 113 ASN G 39 GLN G 113 ASN H 113 ASN I 113 ASN J 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 15036 Z= 0.184 Angle : 0.540 7.489 20400 Z= 0.307 Chirality : 0.039 0.141 2400 Planarity : 0.003 0.033 2640 Dihedral : 4.171 18.685 2028 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.31 % Allowed : 11.26 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.17), residues: 1848 helix: 2.67 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.48 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 52 HIS 0.006 0.002 HIS K 63 PHE 0.007 0.001 PHE C 59 TYR 0.008 0.001 TYR C 16 ARG 0.006 0.000 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 1.881 Fit side-chains REVERT: A 55 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7697 (ptm160) REVERT: A 134 LYS cc_start: 0.7671 (mttp) cc_final: 0.7368 (mttp) REVERT: C 70 ARG cc_start: 0.8351 (ttt180) cc_final: 0.7645 (ttp80) REVERT: C 142 ASP cc_start: 0.7781 (m-30) cc_final: 0.7557 (m-30) REVERT: D 55 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7533 (ptm160) REVERT: E 134 LYS cc_start: 0.7719 (mttp) cc_final: 0.7423 (mttp) REVERT: F 134 LYS cc_start: 0.7664 (mttp) cc_final: 0.7141 (mtpt) REVERT: G 55 ARG cc_start: 0.8244 (ptp90) cc_final: 0.7991 (ptm160) REVERT: H 25 GLU cc_start: 0.6898 (tt0) cc_final: 0.6452 (tp30) REVERT: I 25 GLU cc_start: 0.6882 (tt0) cc_final: 0.6415 (tp30) REVERT: I 134 LYS cc_start: 0.7793 (mttp) cc_final: 0.7318 (mtpt) REVERT: J 101 LYS cc_start: 0.7214 (mttt) cc_final: 0.6958 (mttm) REVERT: K 70 ARG cc_start: 0.8333 (ttt180) cc_final: 0.7690 (ttp80) outliers start: 9 outliers final: 5 residues processed: 294 average time/residue: 1.9205 time to fit residues: 607.4874 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 286 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 99 ASN A 113 ASN C 39 GLN C 113 ASN D 39 GLN E 113 ASN F 36 GLN F 113 ASN G 39 GLN G 113 ASN H 113 ASN I 113 ASN J 99 ASN J 113 ASN L 39 GLN L 99 ASN L 113 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15036 Z= 0.324 Angle : 0.683 8.072 20400 Z= 0.390 Chirality : 0.045 0.194 2400 Planarity : 0.005 0.072 2640 Dihedral : 4.467 19.899 2028 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.37 % Allowed : 11.07 % Favored : 87.56 % 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: 2.70 (0.17), residues: 1848 helix: 2.18 (0.12), residues: 1428 sheet: None (None), residues: 0 loop : 0.53 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 160 HIS 0.009 0.003 HIS B 63 PHE 0.013 0.003 PHE C 59 TYR 0.013 0.003 TYR C 16 ARG 0.009 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 279 time to evaluate : 2.101 Fit side-chains REVERT: A 55 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7866 (ptm160) REVERT: B 25 GLU cc_start: 0.6949 (tt0) cc_final: 0.6495 (tp30) REVERT: C 70 ARG cc_start: 0.8337 (ttt180) cc_final: 0.7645 (ttp80) REVERT: C 142 ASP cc_start: 0.7898 (m-30) cc_final: 0.7638 (m-30) REVERT: D 55 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7741 (ptm160) REVERT: E 134 LYS cc_start: 0.7702 (mttp) cc_final: 0.7451 (mttp) REVERT: F 25 GLU cc_start: 0.6958 (tt0) cc_final: 0.6516 (tp30) REVERT: F 55 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7593 (ptm160) REVERT: F 134 LYS cc_start: 0.7739 (mttp) cc_final: 0.7202 (mtpt) REVERT: H 25 GLU cc_start: 0.6952 (tt0) cc_final: 0.6511 (tp30) REVERT: I 25 GLU cc_start: 0.6970 (tt0) cc_final: 0.6497 (tp30) REVERT: I 134 LYS cc_start: 0.7816 (mttp) cc_final: 0.7348 (mtpt) REVERT: J 101 LYS cc_start: 0.7317 (mttt) cc_final: 0.7052 (mttm) REVERT: K 70 ARG cc_start: 0.8322 (ttt180) cc_final: 0.7685 (ttp80) outliers start: 10 outliers final: 6 residues processed: 281 average time/residue: 1.9386 time to fit residues: 583.0488 Evaluate side-chains 286 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 277 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 113 ASN B 113 ASN C 99 ASN C 113 ASN D 113 ASN E 113 ASN F 36 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN J 113 ASN L 39 GLN L 99 ASN L 113 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15036 Z= 0.218 Angle : 0.584 8.506 20400 Z= 0.332 Chirality : 0.041 0.157 2400 Planarity : 0.004 0.039 2640 Dihedral : 4.304 19.244 2028 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.31 % Allowed : 11.13 % Favored : 87.56 % 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: 3.04 (0.17), residues: 1848 helix: 2.46 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.41 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 52 HIS 0.007 0.002 HIS B 63 PHE 0.009 0.002 PHE C 59 TYR 0.010 0.001 TYR C 16 ARG 0.004 0.001 ARG L 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 283 time to evaluate : 1.810 Fit side-chains REVERT: A 55 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7713 (ptm160) REVERT: B 25 GLU cc_start: 0.6967 (tt0) cc_final: 0.6516 (tp30) REVERT: C 70 ARG cc_start: 0.8349 (ttt180) cc_final: 0.7652 (ttp80) REVERT: C 142 ASP cc_start: 0.7822 (m-30) cc_final: 0.7595 (m-30) REVERT: D 55 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7560 (ptm160) REVERT: E 134 LYS cc_start: 0.7689 (mttp) cc_final: 0.7395 (mttp) REVERT: F 134 LYS cc_start: 0.7704 (mttp) cc_final: 0.7160 (mtpt) REVERT: H 25 GLU cc_start: 0.6906 (tt0) cc_final: 0.6459 (tp30) REVERT: I 25 GLU cc_start: 0.6934 (tt0) cc_final: 0.6474 (tp30) REVERT: I 134 LYS cc_start: 0.7822 (mttp) cc_final: 0.7340 (mtpt) REVERT: J 101 LYS cc_start: 0.7239 (mttt) cc_final: 0.6983 (mttm) REVERT: K 70 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7676 (ttp80) outliers start: 9 outliers final: 6 residues processed: 285 average time/residue: 1.9167 time to fit residues: 584.5244 Evaluate side-chains 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 281 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 113 ASN B 113 ASN C 39 GLN C 99 ASN C 113 ASN D 113 ASN E 113 ASN F 36 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN J 99 ASN J 113 ASN L 39 GLN L 99 ASN L 113 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15036 Z= 0.246 Angle : 0.612 8.515 20400 Z= 0.350 Chirality : 0.042 0.169 2400 Planarity : 0.004 0.041 2640 Dihedral : 4.356 19.312 2028 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.31 % Allowed : 11.07 % Favored : 87.62 % 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: 2.91 (0.17), residues: 1848 helix: 2.37 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.39 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 160 HIS 0.008 0.002 HIS A 63 PHE 0.010 0.002 PHE C 59 TYR 0.011 0.002 TYR C 16 ARG 0.006 0.001 ARG L 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 283 time to evaluate : 1.927 Fit side-chains REVERT: A 55 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7731 (ptm160) REVERT: B 25 GLU cc_start: 0.6946 (tt0) cc_final: 0.6501 (tp30) REVERT: C 70 ARG cc_start: 0.8341 (ttt180) cc_final: 0.7652 (ttp80) REVERT: C 142 ASP cc_start: 0.7830 (m-30) cc_final: 0.7593 (m-30) REVERT: D 55 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7609 (ptm160) REVERT: E 134 LYS cc_start: 0.7684 (mttp) cc_final: 0.7398 (mttp) REVERT: F 134 LYS cc_start: 0.7709 (mttp) cc_final: 0.7167 (mtpt) REVERT: F 142 ASP cc_start: 0.7929 (m-30) cc_final: 0.7669 (m-30) REVERT: H 25 GLU cc_start: 0.6915 (tt0) cc_final: 0.6474 (tp30) REVERT: I 25 GLU cc_start: 0.6941 (tt0) cc_final: 0.6482 (tp30) REVERT: I 134 LYS cc_start: 0.7802 (mttp) cc_final: 0.7325 (mtpt) REVERT: J 101 LYS cc_start: 0.7244 (mttt) cc_final: 0.6986 (mttm) REVERT: K 70 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7680 (ttp80) outliers start: 9 outliers final: 6 residues processed: 285 average time/residue: 1.9238 time to fit residues: 587.2536 Evaluate side-chains 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 281 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 39 GLN C 113 ASN D 113 ASN E 113 ASN F 36 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN J 113 ASN L 39 GLN L 99 ASN L 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15036 Z= 0.220 Angle : 0.585 8.408 20400 Z= 0.332 Chirality : 0.041 0.161 2400 Planarity : 0.004 0.037 2640 Dihedral : 4.303 19.120 2028 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.31 % Allowed : 11.13 % Favored : 87.56 % 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: 3.09 (0.17), residues: 1848 helix: 2.50 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.42 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 52 HIS 0.007 0.002 HIS B 63 PHE 0.008 0.002 PHE C 59 TYR 0.010 0.001 TYR C 16 ARG 0.004 0.001 ARG L 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 283 time to evaluate : 1.859 Fit side-chains REVERT: A 55 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7705 (ptm160) REVERT: B 25 GLU cc_start: 0.6945 (tt0) cc_final: 0.6496 (tp30) REVERT: C 70 ARG cc_start: 0.8343 (ttt180) cc_final: 0.7652 (ttp80) REVERT: C 142 ASP cc_start: 0.7801 (m-30) cc_final: 0.7564 (m-30) REVERT: D 55 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7559 (ptm160) REVERT: E 55 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7752 (ptm160) REVERT: E 134 LYS cc_start: 0.7680 (mttp) cc_final: 0.7395 (mttp) REVERT: F 134 LYS cc_start: 0.7714 (mttp) cc_final: 0.7171 (mtpt) REVERT: H 25 GLU cc_start: 0.6906 (tt0) cc_final: 0.6459 (tp30) REVERT: I 25 GLU cc_start: 0.6935 (tt0) cc_final: 0.6473 (tp30) REVERT: I 134 LYS cc_start: 0.7817 (mttp) cc_final: 0.7339 (mtpt) REVERT: J 101 LYS cc_start: 0.7231 (mttt) cc_final: 0.6975 (mttm) REVERT: K 70 ARG cc_start: 0.8312 (ttt180) cc_final: 0.7677 (ttp80) outliers start: 9 outliers final: 6 residues processed: 285 average time/residue: 1.9291 time to fit residues: 588.2724 Evaluate side-chains 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 280 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 39 GLN C 113 ASN D 113 ASN E 113 ASN F 36 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.172020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.158054 restraints weight = 42492.371| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.09 r_work: 0.3584 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15036 Z= 0.179 Angle : 0.538 8.227 20400 Z= 0.303 Chirality : 0.039 0.138 2400 Planarity : 0.003 0.035 2640 Dihedral : 4.169 18.640 2028 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.31 % Allowed : 11.19 % Favored : 87.50 % 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: 3.47 (0.18), residues: 1848 helix: 2.77 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.54 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 52 HIS 0.006 0.002 HIS B 63 PHE 0.006 0.001 PHE C 59 TYR 0.008 0.001 TYR C 16 ARG 0.012 0.000 ARG G 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8547.86 seconds wall clock time: 150 minutes 10.35 seconds (9010.35 seconds total)