Starting phenix.real_space_refine (version: dev) on Tue Dec 13 13:53:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2022/6zgl_11210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2022/6zgl_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_2022/6zgl_11210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2022/6zgl_11210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2022/6zgl_11210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/12_2022/6zgl_11210.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 16.11, per 1000 atoms: 1.02 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: 7.39 Conformation dependent library (CDL) restraints added in 4.0 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: 0.36 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: 4.40 Time building geometry restraints manager: 7.74 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 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. 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: 3.710 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: 0.000 Extract box with map and model: 6.900 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.140 Process input model: 52.310 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 3.73 % 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 *********************** 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 : 1.909 Fit side-chains outliers start: 48 outliers final: 9 residues processed: 287 average time/residue: 1.7525 time to fit residues: 541.8497 Evaluate side-chains 281 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 272 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.4142 ------------------------------------------------------------------------------- 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: 0.8159 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 : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.37 % 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 *********************** 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 : 1.761 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 300 average time/residue: 1.7353 time to fit residues: 561.3388 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 285 time to evaluate : 1.909 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.1444 time to fit residues: 3.6199 ------------------------------------------------------------------------------- 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: 6.9990 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 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: 2.3990 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 15036 Z= 0.240 Angle : 0.618 9.306 20400 Z= 0.352 Chirality : 0.042 0.156 2400 Planarity : 0.004 0.038 2640 Dihedral : 4.183 19.782 2028 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer Outliers : 1.74 % 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: 3.01 (0.17), residues: 1848 helix: 2.45 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.40 (0.28), residues: 408 *********************** 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 300 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 1.945 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 289 average time/residue: 1.7756 time to fit residues: 552.9101 Evaluate side-chains 285 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1414 time to fit residues: 4.2972 ------------------------------------------------------------------------------- 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: 0.6980 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15036 Z= 0.179 Angle : 0.541 7.775 20400 Z= 0.304 Chirality : 0.039 0.131 2400 Planarity : 0.003 0.040 2640 Dihedral : 4.049 18.249 2028 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer Outliers : 1.31 % 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 (0.17), residues: 1848 helix: 2.70 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.69 (0.28), residues: 396 *********************** 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 294 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 285 time to evaluate : 1.861 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 289 average time/residue: 1.8295 time to fit residues: 571.4878 Evaluate side-chains 285 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1534 time to fit residues: 3.3991 ------------------------------------------------------------------------------- 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: 7.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 113 ASN I 113 ASN K 39 GLN L 39 GLN L 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1776 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= 0.299 Angle : 0.667 8.226 20400 Z= 0.380 Chirality : 0.044 0.173 2400 Planarity : 0.005 0.068 2640 Dihedral : 4.371 19.712 2028 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.62 % 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: 2.73 (0.17), residues: 1848 helix: 2.22 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.37 (0.29), residues: 408 *********************** 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 295 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 1.883 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 286 average time/residue: 1.7976 time to fit residues: 553.1167 Evaluate side-chains 287 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.4546 time to fit residues: 5.3672 ------------------------------------------------------------------------------- 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: 0.8980 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.1930 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= 0.200 Angle : 0.565 7.536 20400 Z= 0.320 Chirality : 0.040 0.144 2400 Planarity : 0.003 0.037 2640 Dihedral : 4.191 18.839 2028 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer Outliers : 1.62 % 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: 3.22 (0.17), residues: 1848 helix: 2.60 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.43 (0.28), residues: 408 *********************** 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 301 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 287 time to evaluate : 1.989 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 290 average time/residue: 1.7439 time to fit residues: 545.3618 Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 7 average time/residue: 0.8152 time to fit residues: 9.1444 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 39 GLN F 113 ASN G 113 ASN H 113 ASN I 113 ASN L 39 GLN L 99 ASN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 15036 Z= 0.292 Angle : 0.660 7.874 20400 Z= 0.377 Chirality : 0.044 0.174 2400 Planarity : 0.005 0.057 2640 Dihedral : 4.399 19.550 2028 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 1.43 % 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: 2.72 (0.17), residues: 1848 helix: 2.23 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.34 (0.29), residues: 408 *********************** 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 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 279 time to evaluate : 1.897 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 283 average time/residue: 1.7955 time to fit residues: 549.0325 Evaluate side-chains 285 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1563 time to fit residues: 3.7990 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 113 ASN C 99 ASN C 113 ASN D 113 ASN E 113 ASN F 113 ASN G 39 GLN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1865 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= 0.229 Angle : 0.601 8.396 20400 Z= 0.341 Chirality : 0.041 0.156 2400 Planarity : 0.004 0.043 2640 Dihedral : 4.299 19.328 2028 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 1.06 % 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: 3.02 (0.17), residues: 1848 helix: 2.45 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.40 (0.29), residues: 408 *********************** 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 287 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 1.824 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 286 average time/residue: 1.8014 time to fit residues: 553.9189 Evaluate side-chains 280 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.5315 ------------------------------------------------------------------------------- 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: 6.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 113 ASN F 113 ASN G 39 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1949 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= 0.195 Angle : 0.561 7.965 20400 Z= 0.317 Chirality : 0.040 0.136 2400 Planarity : 0.003 0.034 2640 Dihedral : 4.191 18.901 2028 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.12 % 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: 3.33 (0.17), residues: 1848 helix: 2.68 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.48 (0.29), residues: 408 *********************** 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 295 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 289 time to evaluate : 1.730 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 292 average time/residue: 1.7608 time to fit residues: 553.1034 Evaluate side-chains 285 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 281 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1442 time to fit residues: 2.9127 ------------------------------------------------------------------------------- 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: 6.9990 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 113 ASN G 39 GLN G 113 ASN H 113 ASN I 113 ASN L 39 GLN L 99 ASN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15036 Z= 0.225 Angle : 0.597 8.541 20400 Z= 0.338 Chirality : 0.041 0.155 2400 Planarity : 0.004 0.040 2640 Dihedral : 4.250 19.246 2028 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 1.06 % 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: 3.15 (0.17), residues: 1848 helix: 2.54 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.43 (0.29), residues: 408 ********************** 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 288 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 283 time to evaluate : 1.884 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 286 average time/residue: 1.8424 time to fit residues: 567.3913 Evaluate side-chains 284 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1399 time to fit residues: 2.9851 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.0170 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 113 ASN F 113 ASN G 39 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.172777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.158977 restraints weight = 42782.703| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.02 r_work: 0.3594 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2036 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= 0.176 Angle : 0.539 8.168 20400 Z= 0.301 Chirality : 0.039 0.135 2400 Planarity : 0.003 0.040 2640 Dihedral : 4.103 18.556 2028 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer Outliers : 1.00 % 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: 3.59 (0.18), residues: 1848 helix: 2.80 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.77 (0.29), residues: 396 =============================================================================== Job complete usr+sys time: 7957.53 seconds wall clock time: 141 minutes 6.02 seconds (8466.02 seconds total)