Starting phenix.real_space_refine on Sun Dec 10 21:48:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2023/6zgl_11210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2023/6zgl_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_11210/12_2023/6zgl_11210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2023/6zgl_11210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2023/6zgl_11210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2023/6zgl_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 15.31, per 1000 atoms: 0.97 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: 7.68 Conformation dependent library (CDL) restraints added in 5.2 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: 1.22 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: 4.72 Time building geometry restraints manager: 8.00 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: 0.010 Normalize map: mean=0, sd=1: 1.830 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: 0.020 Extract box with map and model: 6.390 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 54.760 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.010 ------------------------------------------------------------------------------- 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 : 3.613 Fit side-chains outliers start: 48 outliers final: 9 residues processed: 287 average time/residue: 1.9460 time to fit residues: 600.0807 Evaluate side-chains 281 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 272 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.5135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 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: 1.0384 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15036 Z= 0.184 Angle : 0.564 6.675 20400 Z= 0.317 Chirality : 0.040 0.137 2400 Planarity : 0.003 0.021 2640 Dihedral : 3.943 18.441 2028 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.37 % Allowed : 9.20 % Favored : 89.43 % 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: 3.23 (0.18), residues: 1848 helix: 2.68 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.01 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 52 HIS 0.006 0.002 HIS B 63 PHE 0.010 0.002 PHE L 69 TYR 0.008 0.001 TYR C 16 ARG 0.003 0.001 ARG J 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 306 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 296 time to evaluate : 1.789 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 300 average time/residue: 1.9136 time to fit residues: 616.0440 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 285 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.1422 time to fit residues: 3.5268 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 39 GLN F 113 ASN G 113 ASN H 39 GLN H 113 ASN I 113 ASN J 39 GLN K 39 GLN L 39 GLN L 113 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15036 Z= 0.229 Angle : 0.606 9.303 20400 Z= 0.345 Chirality : 0.042 0.154 2400 Planarity : 0.004 0.036 2640 Dihedral : 4.151 19.650 2028 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.55 % Allowed : 10.63 % Favored : 87.81 % 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: 3.08 (0.17), residues: 1848 helix: 2.49 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.42 (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 0.012 0.002 PHE C 59 TYR 0.010 0.002 TYR C 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 297 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 284 time to evaluate : 1.815 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 289 average time/residue: 1.9492 time to fit residues: 604.0630 Evaluate side-chains 286 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 277 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1521 time to fit residues: 3.6457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 113 ASN D 113 ASN E 113 ASN F 39 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN K 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15036 Z= 0.268 Angle : 0.643 8.891 20400 Z= 0.366 Chirality : 0.043 0.168 2400 Planarity : 0.005 0.051 2640 Dihedral : 4.327 20.395 2028 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.49 % Allowed : 10.39 % Favored : 88.12 % 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: 2.79 (0.17), residues: 1848 helix: 2.28 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 160 HIS 0.008 0.003 HIS B 63 PHE 0.013 0.002 PHE C 59 TYR 0.012 0.002 TYR C 16 ARG 0.008 0.001 ARG G 55 *********************** 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 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 278 time to evaluate : 1.840 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 284 average time/residue: 1.9046 time to fit residues: 579.5837 Evaluate side-chains 283 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1523 time to fit residues: 3.7015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 113 ASN D 113 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 113 ASN K 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15036 Z= 0.159 Angle : 0.505 7.351 20400 Z= 0.284 Chirality : 0.037 0.119 2400 Planarity : 0.003 0.027 2640 Dihedral : 3.991 18.133 2028 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.12 % Allowed : 11.44 % 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: 3.61 (0.18), residues: 1848 helix: 2.82 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.65 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 52 HIS 0.005 0.001 HIS A 63 PHE 0.007 0.001 PHE H 69 TYR 0.006 0.001 TYR C 16 ARG 0.005 0.000 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 304 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 298 time to evaluate : 1.750 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 299 average time/residue: 1.9319 time to fit residues: 619.0670 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 288 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.1413 time to fit residues: 3.4194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 174 optimal weight: 0.0040 chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 B 113 ASN C 39 GLN C 113 ASN D 39 GLN E 113 ASN F 39 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN J 39 GLN K 39 GLN K 113 ASN L 113 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15036 Z= 0.172 Angle : 0.521 8.072 20400 Z= 0.294 Chirality : 0.038 0.130 2400 Planarity : 0.003 0.022 2640 Dihedral : 3.996 18.397 2028 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.18 % Allowed : 12.00 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.18), residues: 1848 helix: 2.88 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.84 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 52 HIS 0.006 0.002 HIS A 63 PHE 0.006 0.001 PHE C 59 TYR 0.007 0.001 TYR L 16 ARG 0.004 0.000 ARG E 35 *********************** 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 300 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 293 time to evaluate : 1.845 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 294 average time/residue: 2.0185 time to fit residues: 635.4035 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 290 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1432 time to fit residues: 2.9202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 0.0020 chunk 99 optimal weight: 0.0470 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN B 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN F 39 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15036 Z= 0.164 Angle : 0.503 7.591 20400 Z= 0.284 Chirality : 0.038 0.126 2400 Planarity : 0.003 0.021 2640 Dihedral : 3.946 18.268 2028 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.18 % Allowed : 12.19 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.18), residues: 1848 helix: 2.89 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.81 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 52 HIS 0.006 0.002 HIS D 63 PHE 0.006 0.001 PHE L 69 TYR 0.006 0.001 TYR C 16 ARG 0.004 0.000 ARG E 35 *********************** 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 298 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 291 time to evaluate : 1.914 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 293 average time/residue: 1.9682 time to fit residues: 617.6459 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 289 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.9315 time to fit residues: 4.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 113 ASN D 39 GLN D 113 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 39 GLN G 113 ASN H 113 ASN I 113 ASN K 39 GLN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15036 Z= 0.157 Angle : 0.489 7.907 20400 Z= 0.276 Chirality : 0.037 0.123 2400 Planarity : 0.003 0.020 2640 Dihedral : 3.886 18.094 2028 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.00 % Allowed : 12.13 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.18), residues: 1848 helix: 2.97 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.85 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 52 HIS 0.005 0.001 HIS D 63 PHE 0.006 0.001 PHE C 69 TYR 0.006 0.001 TYR C 16 ARG 0.004 0.000 ARG E 35 *********************** 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 298 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 294 time to evaluate : 2.139 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 296 average time/residue: 1.9462 time to fit residues: 617.9370 Evaluate side-chains 295 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1423 time to fit residues: 2.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN 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 113 ASN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15036 Z= 0.198 Angle : 0.545 7.962 20400 Z= 0.310 Chirality : 0.040 0.157 2400 Planarity : 0.003 0.027 2640 Dihedral : 4.060 18.866 2028 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.06 % Allowed : 12.50 % Favored : 86.44 % 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: 3.57 (0.18), residues: 1848 helix: 2.76 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.85 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 52 HIS 0.007 0.002 HIS A 63 PHE 0.009 0.002 PHE C 59 TYR 0.009 0.001 TYR C 16 ARG 0.004 0.001 ARG E 35 *********************** 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 294 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 289 time to evaluate : 1.663 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 291 average time/residue: 1.9470 time to fit residues: 608.0097 Evaluate side-chains 291 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1490 time to fit residues: 3.0122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 113 ASN E 39 GLN 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 113 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 ASN K 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15036 Z= 0.155 Angle : 0.489 7.771 20400 Z= 0.276 Chirality : 0.037 0.118 2400 Planarity : 0.003 0.019 2640 Dihedral : 3.932 18.158 2028 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.93 % Allowed : 12.56 % Favored : 86.50 % 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: 3.84 (0.18), residues: 1848 helix: 2.95 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.87 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 52 HIS 0.005 0.002 HIS A 63 PHE 0.006 0.001 PHE L 69 TYR 0.006 0.001 TYR C 16 ARG 0.004 0.000 ARG E 35 ********************** 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 294 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 1.910 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 293 average time/residue: 2.0166 time to fit residues: 632.5569 Evaluate side-chains 295 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.7418 time to fit residues: 4.2941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 39 GLN C 113 ASN D 39 GLN D 113 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 113 ASN I 39 GLN I 113 ASN L 39 GLN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.160086 restraints weight = 44124.512| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.01 r_work: 0.3617 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15036 Z= 0.163 Angle : 0.500 7.756 20400 Z= 0.283 Chirality : 0.038 0.127 2400 Planarity : 0.003 0.020 2640 Dihedral : 3.938 18.322 2028 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.87 % Allowed : 12.94 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.18), residues: 1848 helix: 2.91 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.83 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 52 HIS 0.006 0.002 HIS D 63 PHE 0.006 0.001 PHE H 59 TYR 0.007 0.001 TYR C 16 ARG 0.004 0.000 ARG E 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8742.26 seconds wall clock time: 154 minutes 40.67 seconds (9280.67 seconds total)