Starting phenix.real_space_refine on Fri Sep 27 06:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/09_2024/6zgl_11210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/09_2024/6zgl_11210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/09_2024/6zgl_11210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/09_2024/6zgl_11210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/09_2024/6zgl_11210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgl_11210/09_2024/6zgl_11210.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15760 Number of models: 1 Model: "" Number of chains: 13 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: "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} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.85, per 1000 atoms: 0.37 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 3.5 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: 1.17 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: 4.69 Time building geometry restraints manager: 4.83 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: 0.00 - 1.68: 15613 1.68 - 3.35: 3938 3.35 - 5.03: 669 5.03 - 6.70: 156 6.70 - 8.38: 24 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 3.040 nonbonded pdb=" OD1 ASP I 75 " pdb=" O HOH I 201 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP H 75 " pdb=" O HOH H 201 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP J 75 " pdb=" O HOH J 201 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP L 75 " pdb=" O HOH L 201 " model vdw 2.204 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'B' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'C' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'D' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'E' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'F' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'G' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'H' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'I' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'J' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'K' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) selection = (chain 'L' and (resid 14 through 30 or resid 32 through 156 or resid 158 through \ 167)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 34.820 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.067 15036 Z= 0.845 Angle : 1.549 8.379 20400 Z= 1.068 Chirality : 0.115 0.532 2400 Planarity : 0.010 0.044 2640 Dihedral : 15.524 87.169 5592 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.73 % Allowed : 8.21 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 1848 helix: 0.45 (0.12), residues: 1404 sheet: None (None), residues: 0 loop : -0.77 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.013 TRP I 160 HIS 0.010 0.003 HIS G 51 PHE 0.081 0.012 PHE F 59 TYR 0.036 0.014 TYR J 16 ARG 0.031 0.005 ARG L 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 275 time to evaluate : 1.741 Fit side-chains REVERT: A 25 GLU cc_start: 0.6760 (tt0) cc_final: 0.6329 (tp30) REVERT: A 134 LYS cc_start: 0.7747 (mttp) cc_final: 0.7534 (mttt) REVERT: B 25 GLU cc_start: 0.6780 (tt0) cc_final: 0.6328 (tp30) REVERT: B 142 ASP cc_start: 0.7973 (m-30) cc_final: 0.7734 (m-30) REVERT: C 25 GLU cc_start: 0.6764 (tt0) cc_final: 0.6331 (tp30) REVERT: C 101 LYS cc_start: 0.7221 (mttt) cc_final: 0.6932 (mttm) REVERT: D 101 LYS cc_start: 0.7262 (mttt) cc_final: 0.7023 (mttm) REVERT: D 134 LYS cc_start: 0.7748 (mttp) cc_final: 0.7537 (mttp) REVERT: D 138 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: E 22 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (p) REVERT: E 25 GLU cc_start: 0.6758 (tt0) cc_final: 0.6317 (tp30) REVERT: E 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7486 (mttp) REVERT: F 25 GLU cc_start: 0.6737 (tt0) cc_final: 0.6352 (tp30) REVERT: F 70 ARG cc_start: 0.8416 (ttt180) cc_final: 0.7465 (ttp80) REVERT: F 75 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (t70) REVERT: F 101 LYS cc_start: 0.7181 (mttt) cc_final: 0.6896 (mttm) REVERT: F 134 LYS cc_start: 0.7664 (mttp) cc_final: 0.7463 (mttt) REVERT: G 25 GLU cc_start: 0.6671 (tt0) cc_final: 0.6261 (tp30) REVERT: G 35 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7730 (mtm110) REVERT: G 134 LYS cc_start: 0.7695 (mttp) cc_final: 0.7478 (mttm) REVERT: H 24 SER cc_start: 0.7174 (OUTLIER) cc_final: 0.6967 (p) REVERT: H 25 GLU cc_start: 0.6767 (tt0) cc_final: 0.6349 (tp30) REVERT: H 70 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8116 (ttt180) REVERT: H 75 ASP cc_start: 0.8558 (m-30) cc_final: 0.8269 (t70) REVERT: H 120 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8180 (mm-30) REVERT: H 138 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: H 142 ASP cc_start: 0.7942 (m-30) cc_final: 0.7644 (m-30) REVERT: I 25 GLU cc_start: 0.6744 (tt0) cc_final: 0.6359 (tp30) REVERT: I 101 LYS cc_start: 0.7180 (mttt) cc_final: 0.6910 (mttm) REVERT: J 35 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: J 101 LYS cc_start: 0.7248 (mttt) cc_final: 0.7033 (mttm) REVERT: J 134 LYS cc_start: 0.7731 (mttp) cc_final: 0.7489 (mttp) REVERT: J 142 ASP cc_start: 0.8001 (m-30) cc_final: 0.7790 (m-30) REVERT: K 25 GLU cc_start: 0.6860 (tt0) cc_final: 0.6367 (tp30) REVERT: K 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7154 (mtpt) REVERT: K 142 ASP cc_start: 0.8026 (m-30) cc_final: 0.7781 (m-30) REVERT: L 25 GLU cc_start: 0.6769 (tt0) cc_final: 0.6321 (tp30) REVERT: L 101 LYS cc_start: 0.7307 (mttt) cc_final: 0.7052 (mttm) REVERT: L 142 ASP cc_start: 0.7957 (m-30) cc_final: 0.7726 (m-30) outliers start: 48 outliers final: 9 residues processed: 287 average time/residue: 1.8349 time to fit residues: 565.0258 Evaluate side-chains 288 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 15036 Z= 0.189 Angle : 0.575 6.885 20400 Z= 0.326 Chirality : 0.041 0.129 2400 Planarity : 0.004 0.019 2640 Dihedral : 4.657 29.564 2053 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.75 % Allowed : 9.64 % Favored : 89.61 % 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: 3.18 (0.18), residues: 1848 helix: 2.55 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.35 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 160 HIS 0.006 0.002 HIS K 63 PHE 0.010 0.002 PHE L 69 TYR 0.008 0.001 TYR C 16 ARG 0.003 0.001 ARG K 18 *********************** 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 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.769 Fit side-chains REVERT: A 35 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7472 (ttp80) REVERT: A 134 LYS cc_start: 0.7647 (mttp) cc_final: 0.7407 (mttp) REVERT: B 25 GLU cc_start: 0.6778 (tt0) cc_final: 0.6334 (tp30) REVERT: E 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7525 (mttm) REVERT: F 25 GLU cc_start: 0.6794 (tt0) cc_final: 0.6362 (tp30) REVERT: F 70 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7455 (ttp80) REVERT: F 75 ASP cc_start: 0.8395 (m-30) cc_final: 0.8072 (t70) REVERT: F 134 LYS cc_start: 0.7641 (mttp) cc_final: 0.7079 (mtpt) REVERT: G 134 LYS cc_start: 0.7676 (mttp) cc_final: 0.7418 (mttp) REVERT: H 25 GLU cc_start: 0.6811 (tt0) cc_final: 0.6345 (tp30) REVERT: H 35 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7537 (ttp80) REVERT: H 134 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7257 (mtpt) REVERT: I 25 GLU cc_start: 0.6815 (tt0) cc_final: 0.6382 (tp30) REVERT: I 134 LYS cc_start: 0.7712 (mttp) cc_final: 0.7308 (mtpt) REVERT: J 55 ARG cc_start: 0.8174 (ptp-110) cc_final: 0.7960 (ptm160) REVERT: J 101 LYS cc_start: 0.7237 (mttt) cc_final: 0.6926 (mttm) REVERT: J 134 LYS cc_start: 0.7668 (mttp) cc_final: 0.7450 (mttp) REVERT: K 55 ARG cc_start: 0.8179 (ptp90) cc_final: 0.7968 (ptm160) REVERT: K 134 LYS cc_start: 0.7715 (mttp) cc_final: 0.7502 (mtmm) REVERT: L 35 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7468 (ttp80) REVERT: L 65 MET cc_start: 0.8595 (ttp) cc_final: 0.8391 (ttp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 1.9314 time to fit residues: 596.9548 Evaluate side-chains 269 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 39 GLN D 113 ASN E 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 113 ASN J 39 GLN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15036 Z= 0.256 Angle : 0.635 8.278 20400 Z= 0.363 Chirality : 0.043 0.161 2400 Planarity : 0.004 0.039 2640 Dihedral : 4.273 19.008 2028 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.12 % Allowed : 9.89 % Favored : 88.99 % 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: 2.92 (0.17), residues: 1848 helix: 2.36 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.48 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 52 HIS 0.008 0.002 HIS K 63 PHE 0.014 0.002 PHE C 59 TYR 0.011 0.002 TYR C 16 ARG 0.005 0.001 ARG L 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 284 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 1.836 Fit side-chains REVERT: A 134 LYS cc_start: 0.7726 (mttp) cc_final: 0.7512 (mttp) REVERT: B 25 GLU cc_start: 0.6821 (tt0) cc_final: 0.6333 (tp30) REVERT: E 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7465 (mttp) REVERT: F 134 LYS cc_start: 0.7666 (mttp) cc_final: 0.7089 (mtpt) REVERT: F 142 ASP cc_start: 0.7878 (m-30) cc_final: 0.7648 (m-30) REVERT: H 25 GLU cc_start: 0.6850 (tt0) cc_final: 0.6377 (tp30) REVERT: I 25 GLU cc_start: 0.6891 (tt0) cc_final: 0.6433 (tp30) REVERT: I 134 LYS cc_start: 0.7830 (mttp) cc_final: 0.7352 (mtpt) REVERT: J 55 ARG cc_start: 0.8218 (ptp-170) cc_final: 0.7991 (ptm160) REVERT: J 134 LYS cc_start: 0.7697 (mttp) cc_final: 0.7466 (mttp) REVERT: K 55 ARG cc_start: 0.8221 (ptp90) cc_final: 0.8007 (ptm160) outliers start: 6 outliers final: 3 residues processed: 278 average time/residue: 1.9528 time to fit residues: 581.0446 Evaluate side-chains 276 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 273 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 113 ASN D 113 ASN E 39 GLN E 113 ASN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 15036 Z= 0.160 Angle : 0.511 7.639 20400 Z= 0.289 Chirality : 0.038 0.112 2400 Planarity : 0.003 0.016 2640 Dihedral : 4.045 18.266 2028 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.87 % Allowed : 11.32 % 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: 3.56 (0.18), residues: 1848 helix: 2.76 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.73 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 52 HIS 0.005 0.001 HIS H 63 PHE 0.008 0.001 PHE H 69 TYR 0.006 0.001 TYR C 16 ARG 0.003 0.000 ARG E 35 *********************** 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 308 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 1.739 Fit side-chains REVERT: A 35 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7406 (ttp80) REVERT: A 70 ARG cc_start: 0.8369 (tpt170) cc_final: 0.7642 (ttp80) REVERT: A 134 LYS cc_start: 0.7661 (mttp) cc_final: 0.7132 (mtpt) REVERT: B 35 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7337 (ttp80) REVERT: B 70 ARG cc_start: 0.8481 (tpt170) cc_final: 0.7985 (ttt-90) REVERT: C 35 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7496 (ttp80) REVERT: F 134 LYS cc_start: 0.7588 (mttp) cc_final: 0.6982 (mtpt) REVERT: G 35 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7351 (ttp80) REVERT: H 120 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8117 (mm-30) REVERT: I 25 GLU cc_start: 0.6832 (tt0) cc_final: 0.6371 (tp30) REVERT: I 35 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7433 (ttp80) REVERT: I 134 LYS cc_start: 0.7666 (mttp) cc_final: 0.7276 (mtpt) REVERT: J 35 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7406 (ttp80) REVERT: L 35 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7403 (ttp80) outliers start: 2 outliers final: 1 residues processed: 306 average time/residue: 1.7972 time to fit residues: 590.1739 Evaluate side-chains 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.0370 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 39 GLN C 113 ASN D 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15036 Z= 0.189 Angle : 0.548 8.993 20400 Z= 0.309 Chirality : 0.040 0.130 2400 Planarity : 0.003 0.025 2640 Dihedral : 4.100 18.842 2028 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.37 % Allowed : 11.19 % 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: 3.53 (0.18), residues: 1848 helix: 2.72 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.92 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 52 HIS 0.006 0.002 HIS A 63 PHE 0.009 0.002 PHE C 59 TYR 0.008 0.001 TYR C 16 ARG 0.003 0.000 ARG L 124 *********************** 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 303 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 293 time to evaluate : 1.960 Fit side-chains REVERT: A 35 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7498 (ttp80) REVERT: A 55 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7365 (ptm160) REVERT: A 134 LYS cc_start: 0.7666 (mttp) cc_final: 0.7432 (mttp) REVERT: B 35 ARG cc_start: 0.7706 (mtp-110) cc_final: 0.7447 (ttp80) REVERT: C 70 ARG cc_start: 0.8411 (ttt180) cc_final: 0.7695 (ttp80) REVERT: F 134 LYS cc_start: 0.7614 (mttp) cc_final: 0.7043 (mtpt) REVERT: H 120 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8101 (mm-30) REVERT: I 25 GLU cc_start: 0.6882 (tt0) cc_final: 0.6427 (tp30) REVERT: I 134 LYS cc_start: 0.7701 (mttp) cc_final: 0.7279 (mtpt) REVERT: J 35 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.7404 (ttp80) outliers start: 10 outliers final: 2 residues processed: 293 average time/residue: 1.9367 time to fit residues: 608.2631 Evaluate side-chains 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 287 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 0.0070 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15036 Z= 0.239 Angle : 0.606 8.226 20400 Z= 0.344 Chirality : 0.042 0.155 2400 Planarity : 0.004 0.037 2640 Dihedral : 4.260 19.431 2028 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.49 % Allowed : 10.57 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.17), residues: 1848 helix: 2.45 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.87 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 160 HIS 0.008 0.002 HIS K 63 PHE 0.012 0.002 PHE C 59 TYR 0.011 0.002 TYR C 16 ARG 0.005 0.001 ARG L 124 *********************** 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 295 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 283 time to evaluate : 1.969 Fit side-chains REVERT: A 55 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7402 (ptm160) REVERT: A 134 LYS cc_start: 0.7682 (mttp) cc_final: 0.7429 (mttt) REVERT: F 134 LYS cc_start: 0.7640 (mttp) cc_final: 0.7097 (mtpt) REVERT: F 142 ASP cc_start: 0.7868 (m-30) cc_final: 0.7643 (m-30) REVERT: I 25 GLU cc_start: 0.6945 (tt0) cc_final: 0.6478 (tp30) REVERT: I 134 LYS cc_start: 0.7804 (mttp) cc_final: 0.7329 (mtpt) REVERT: J 55 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7560 (ptm160) outliers start: 12 outliers final: 3 residues processed: 283 average time/residue: 1.9757 time to fit residues: 598.7019 Evaluate side-chains 284 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15036 Z= 0.194 Angle : 0.556 7.797 20400 Z= 0.315 Chirality : 0.040 0.136 2400 Planarity : 0.003 0.027 2640 Dihedral : 4.183 19.056 2028 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.37 % Allowed : 10.39 % Favored : 88.25 % 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: 3.40 (0.18), residues: 1848 helix: 2.62 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.90 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 52 HIS 0.007 0.002 HIS B 63 PHE 0.009 0.002 PHE C 59 TYR 0.008 0.001 TYR C 16 ARG 0.003 0.000 ARG H 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 287 time to evaluate : 1.940 Fit side-chains REVERT: A 35 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7525 (ttp80) REVERT: A 55 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7354 (ptm160) REVERT: A 134 LYS cc_start: 0.7657 (mttp) cc_final: 0.7402 (mttt) REVERT: B 35 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7439 (ttp80) REVERT: B 70 ARG cc_start: 0.8466 (tpt170) cc_final: 0.7992 (ttt-90) REVERT: C 70 ARG cc_start: 0.8407 (ttt180) cc_final: 0.7693 (ttp80) REVERT: F 134 LYS cc_start: 0.7617 (mttp) cc_final: 0.7064 (mtpt) REVERT: I 25 GLU cc_start: 0.6894 (tt0) cc_final: 0.6426 (tp30) REVERT: I 134 LYS cc_start: 0.7769 (mttp) cc_final: 0.7307 (mtpt) REVERT: J 55 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7543 (ptm160) outliers start: 10 outliers final: 4 residues processed: 287 average time/residue: 1.9617 time to fit residues: 602.8940 Evaluate side-chains 292 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 286 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 15036 Z= 0.173 Angle : 0.528 7.506 20400 Z= 0.297 Chirality : 0.039 0.121 2400 Planarity : 0.003 0.036 2640 Dihedral : 4.098 18.844 2028 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.06 % Allowed : 11.13 % 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: 3.53 (0.18), residues: 1848 helix: 2.72 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.85 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 52 HIS 0.006 0.002 HIS B 63 PHE 0.006 0.001 PHE L 69 TYR 0.007 0.001 TYR C 16 ARG 0.008 0.000 ARG G 55 *********************** 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 297 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 1.727 Fit side-chains REVERT: A 35 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.7467 (ttp80) REVERT: A 55 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7366 (ptm160) REVERT: A 134 LYS cc_start: 0.7649 (mttp) cc_final: 0.7029 (mtpt) REVERT: B 35 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7390 (ttp80) REVERT: B 70 ARG cc_start: 0.8477 (tpt170) cc_final: 0.8006 (ttt-90) REVERT: C 70 ARG cc_start: 0.8403 (ttt180) cc_final: 0.7694 (ttp80) REVERT: F 134 LYS cc_start: 0.7602 (mttp) cc_final: 0.7046 (mtpt) REVERT: G 55 ARG cc_start: 0.8149 (ptp90) cc_final: 0.7870 (ptm160) REVERT: H 140 LYS cc_start: 0.6870 (mmtt) cc_final: 0.6250 (mtmm) REVERT: I 25 GLU cc_start: 0.6883 (tt0) cc_final: 0.6418 (tp30) REVERT: I 134 LYS cc_start: 0.7680 (mttp) cc_final: 0.7271 (mtpt) REVERT: J 35 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7295 (ttp80) outliers start: 5 outliers final: 2 residues processed: 292 average time/residue: 1.9176 time to fit residues: 599.3769 Evaluate side-chains 288 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN J 39 GLN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15036 Z= 0.265 Angle : 0.631 8.012 20400 Z= 0.359 Chirality : 0.043 0.174 2400 Planarity : 0.004 0.049 2640 Dihedral : 4.323 19.521 2028 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.18 % Allowed : 10.95 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.17), residues: 1848 helix: 2.35 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.84 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 160 HIS 0.008 0.003 HIS B 63 PHE 0.013 0.002 PHE C 59 TYR 0.011 0.002 TYR C 16 ARG 0.010 0.001 ARG G 55 *********************** 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 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 283 time to evaluate : 2.221 Fit side-chains REVERT: A 55 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7707 (ptm160) REVERT: A 134 LYS cc_start: 0.7674 (mttp) cc_final: 0.7435 (mttt) REVERT: B 35 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7455 (ttp80) REVERT: C 70 ARG cc_start: 0.8382 (ttt180) cc_final: 0.8041 (ttt-90) REVERT: F 25 GLU cc_start: 0.6992 (tt0) cc_final: 0.6514 (tp30) REVERT: F 134 LYS cc_start: 0.7665 (mttp) cc_final: 0.7148 (mtpt) REVERT: F 142 ASP cc_start: 0.7873 (m-30) cc_final: 0.7640 (m-30) REVERT: G 55 ARG cc_start: 0.8233 (ptp90) cc_final: 0.7965 (ptm160) REVERT: I 25 GLU cc_start: 0.6958 (tt0) cc_final: 0.6487 (tp30) REVERT: I 134 LYS cc_start: 0.7802 (mttp) cc_final: 0.7341 (mtpt) REVERT: J 55 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7571 (ptm160) outliers start: 7 outliers final: 3 residues processed: 284 average time/residue: 1.9801 time to fit residues: 602.2250 Evaluate side-chains 282 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 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 99 ASN A 113 ASN B 113 ASN C 39 GLN C 99 ASN C 113 ASN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1887 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= 0.231 Angle : 0.603 8.969 20400 Z= 0.341 Chirality : 0.042 0.155 2400 Planarity : 0.004 0.049 2640 Dihedral : 4.295 19.311 2028 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.12 % Allowed : 10.95 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.17), residues: 1848 helix: 2.41 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.82 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 160 HIS 0.008 0.002 HIS K 63 PHE 0.011 0.002 PHE C 59 TYR 0.010 0.002 TYR C 16 ARG 0.009 0.001 ARG G 55 ********************** 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: 6 poor density : 282 time to evaluate : 1.802 Fit side-chains REVERT: A 55 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7369 (ptm160) REVERT: A 134 LYS cc_start: 0.7643 (mttp) cc_final: 0.7389 (mttt) REVERT: B 35 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7440 (ttp80) REVERT: F 134 LYS cc_start: 0.7676 (mttp) cc_final: 0.7130 (mtpt) REVERT: F 142 ASP cc_start: 0.7858 (m-30) cc_final: 0.7634 (m-30) REVERT: G 55 ARG cc_start: 0.8218 (ptp90) cc_final: 0.7955 (ptm160) REVERT: I 25 GLU cc_start: 0.6948 (tt0) cc_final: 0.6476 (tp30) REVERT: I 134 LYS cc_start: 0.7800 (mttp) cc_final: 0.7328 (mtpt) REVERT: J 55 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7558 (ptm160) outliers start: 6 outliers final: 3 residues processed: 283 average time/residue: 1.9463 time to fit residues: 589.5111 Evaluate side-chains 284 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 113 ASN C 39 GLN C 113 ASN D 113 ASN E 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.172536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.158763 restraints weight = 41713.342| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.04 r_work: 0.3591 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15036 Z= 0.208 Angle : 0.577 8.095 20400 Z= 0.326 Chirality : 0.041 0.147 2400 Planarity : 0.004 0.047 2640 Dihedral : 4.248 19.204 2028 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.12 % Allowed : 10.88 % Favored : 88.00 % 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: 3.29 (0.18), residues: 1848 helix: 2.54 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.86 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 52 HIS 0.007 0.002 HIS H 63 PHE 0.009 0.002 PHE C 59 TYR 0.009 0.001 TYR C 16 ARG 0.009 0.001 ARG G 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8658.84 seconds wall clock time: 150 minutes 42.40 seconds (9042.40 seconds total)