Starting phenix.real_space_refine on Sun Sep 13 05:46:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vl6_21231/09_2026/6vl6_21231.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vl6_21231/09_2026/6vl6_21231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vl6_21231/09_2026/6vl6_21231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vl6_21231/09_2026/6vl6_21231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vl6_21231/09_2026/6vl6_21231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vl6_21231/09_2026/6vl6_21231.map" } resolution = 4.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 13788 2.51 5 N 3564 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21504 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Restraints were copied for chains: C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 2.80, per 1000 atoms: 0.13 Number of scatterers: 21504 At special positions: 0 Unit cell: (162.15, 158.7, 156.4, 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 4116 8.00 N 3564 7.00 C 13788 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 36 through 50 Processing helix chain 'N' and resid 52 through 67 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 86 through 99 Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 56 through 71 Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 90 through 105 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 18 through 33 Processing helix chain 'P' and resid 36 through 50 Processing helix chain 'P' and resid 52 through 67 Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 40 through 55 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 90 through 105 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'Q' and resid 3 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 86 through 99 Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 40 through 55 Processing helix chain 'G' and resid 56 through 71 Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 90 through 105 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'R' and resid 3 through 16 Processing helix chain 'R' and resid 18 through 33 Processing helix chain 'R' and resid 36 through 50 Processing helix chain 'R' and resid 52 through 67 Processing helix chain 'R' and resid 70 through 84 Processing helix chain 'R' and resid 86 through 99 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 56 through 71 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 90 through 105 Processing helix chain 'H' and resid 108 through 122 Processing helix chain 'S' and resid 3 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 86 through 99 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 40 through 55 Processing helix chain 'I' and resid 56 through 71 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 90 through 105 Processing helix chain 'I' and resid 108 through 122 Processing helix chain 'T' and resid 3 through 16 Processing helix chain 'T' and resid 18 through 33 Processing helix chain 'T' and resid 36 through 50 Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 86 through 99 Processing helix chain 'J' and resid 5 through 20 Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 40 through 55 Processing helix chain 'J' and resid 56 through 71 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 90 through 105 Processing helix chain 'J' and resid 108 through 122 Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 86 through 99 Processing helix chain 'K' and resid 5 through 20 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 40 through 55 Processing helix chain 'K' and resid 56 through 71 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 90 through 105 Processing helix chain 'K' and resid 108 through 122 Processing helix chain 'V' and resid 3 through 16 Processing helix chain 'V' and resid 18 through 33 Processing helix chain 'V' and resid 36 through 50 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 70 through 84 Processing helix chain 'V' and resid 86 through 99 Processing helix chain 'L' and resid 5 through 20 Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 40 through 55 Processing helix chain 'L' and resid 56 through 71 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 90 through 105 Processing helix chain 'L' and resid 108 through 122 Processing helix chain 'W' and resid 3 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 86 through 99 Processing helix chain 'M' and resid 5 through 20 Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 40 through 55 Processing helix chain 'M' and resid 56 through 71 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 108 through 122 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 18 through 33 Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 70 through 84 Processing helix chain 'X' and resid 86 through 99 1764 hydrogen bonds defined for protein. 5292 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: 4.13 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4212 1.32 - 1.44: 6379 1.44 - 1.56: 11225 1.56 - 1.68: 84 1.68 - 1.81: 72 Bond restraints: 21972 Sorted by residual: bond pdb=" NE1 TRP O 40 " pdb=" CE2 TRP O 40 " ideal model delta sigma weight residual 1.370 1.326 0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" NE1 TRP U 40 " pdb=" CE2 TRP U 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP Q 40 " pdb=" CE2 TRP Q 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP N 40 " pdb=" CE2 TRP N 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP B 40 " pdb=" CE2 TRP B 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.55e+01 ... (remaining 21967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 23496 1.64 - 3.27: 5137 3.27 - 4.91: 888 4.91 - 6.55: 155 6.55 - 8.18: 48 Bond angle restraints: 29724 Sorted by residual: angle pdb=" C ASP S 33 " pdb=" N PRO S 34 " pdb=" CA PRO S 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.97e+01 angle pdb=" C ASP T 33 " pdb=" N PRO T 34 " pdb=" CA PRO T 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.96e+01 angle pdb=" C ASP N 33 " pdb=" N PRO N 34 " pdb=" CA PRO N 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP R 33 " pdb=" N PRO R 34 " pdb=" CA PRO R 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP W 33 " pdb=" N PRO W 34 " pdb=" CA PRO W 34 " ideal model delta sigma weight residual 119.82 127.98 -8.16 9.80e-01 1.04e+00 6.93e+01 ... (remaining 29719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12386 17.11 - 34.22: 539 34.22 - 51.33: 107 51.33 - 68.43: 48 68.43 - 85.54: 12 Dihedral angle restraints: 13092 sinusoidal: 5196 harmonic: 7896 Sorted by residual: dihedral pdb=" CB MET L 17 " pdb=" CG MET L 17 " pdb=" SD MET L 17 " pdb=" CE MET L 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.36 -39.36 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET F 17 " pdb=" CG MET F 17 " pdb=" SD MET F 17 " pdb=" CE MET F 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET J 17 " pdb=" CG MET J 17 " pdb=" SD MET J 17 " pdb=" CE MET J 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1719 0.065 - 0.130: 773 0.130 - 0.195: 398 0.195 - 0.260: 49 0.260 - 0.325: 25 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA ASN E 80 " pdb=" N ASN E 80 " pdb=" C ASN E 80 " pdb=" CB ASN E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ASN J 80 " pdb=" N ASN J 80 " pdb=" C ASN J 80 " pdb=" CB ASN J 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN K 80 " pdb=" N ASN K 80 " pdb=" C ASN K 80 " pdb=" CB ASN K 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2961 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 59 " -0.044 2.00e-02 2.50e+03 2.22e-02 9.84e+00 pdb=" CG TYR V 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR V 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR V 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR V 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR V 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR V 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 59 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 59 " 0.044 2.00e-02 2.50e+03 2.21e-02 9.75e+00 pdb=" CG TYR R 59 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR R 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 59 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR R 59 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR R 59 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 59 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR R 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 59 " -0.044 2.00e-02 2.50e+03 2.21e-02 9.73e+00 pdb=" CG TYR T 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR T 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR T 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR T 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR T 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR T 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 59 " -0.024 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 10121 2.92 - 3.42: 23687 3.42 - 3.91: 39439 3.91 - 4.41: 49797 4.41 - 4.90: 71062 Nonbonded interactions: 194106 Sorted by model distance: nonbonded pdb=" NZ LYS D 99 " pdb=" OD2 ASP O 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS C 99 " pdb=" OD2 ASP N 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS L 99 " pdb=" OD2 ASP W 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS A 99 " pdb=" OD2 ASP B 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS H 99 " pdb=" OD2 ASP S 88 " model vdw 2.431 3.120 ... (remaining 194101 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.180 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.540 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.019 0.086 21972 Z= 1.051 Angle : 1.456 8.182 29724 Z= 1.015 Chirality : 0.089 0.325 2964 Planarity : 0.008 0.041 3888 Dihedral : 11.376 85.543 8148 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 2592 helix: 0.53 (0.09), residues: 2412 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 32 TYR 0.044 0.008 TYR V 59 TRP 0.016 0.006 TRP B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.01867 / 1.05 (21972) covalent geometry : angle 1.45581 / 1.02 (29724) hydrogen bonds : bond 0.13473 / 8.86 ( 1764) hydrogen bonds : angle 5.34972 / 3.86 ( 5292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.9149 (mmt) cc_final: 0.8679 (mtm) REVERT: A 32 LEU cc_start: 0.9706 (mt) cc_final: 0.9105 (tp) REVERT: A 108 ASN cc_start: 0.9462 (t0) cc_final: 0.8999 (t0) REVERT: A 110 ASP cc_start: 0.9268 (m-30) cc_final: 0.8932 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0981 time to fit residues: 3.9371 Evaluate side-chains 14 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.036 Evaluate side-chains 31 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 33 ASP cc_start: 0.9175 (t0) cc_final: 0.8910 (t0) REVERT: B 36 ASN cc_start: 0.9184 (t0) cc_final: 0.8950 (t0) REVERT: B 67 ASP cc_start: 0.9240 (t0) cc_final: 0.9023 (t0) REVERT: B 86 LYS cc_start: 0.9005 (mptt) cc_final: 0.8735 (mmtt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1355 time to fit residues: 4.3396 Evaluate side-chains 17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.033109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026402 restraints weight = 6760.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.027645 restraints weight = 4092.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028522 restraints weight = 2787.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029293 restraints weight = 2065.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.029889 restraints weight = 1562.953| |-----------------------------------------------------------------------------| r_work (final): 0.2636 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.026701 restraints weight = 6048.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.027883 restraints weight = 3489.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028776 restraints weight = 2280.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.029404 restraints weight = 1613.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.029872 restraints weight = 1221.415| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21972 Z= 0.151 Angle : 0.600 5.613 29724 Z= 0.320 Chirality : 0.041 0.141 2964 Planarity : 0.005 0.033 3888 Dihedral : 3.937 12.450 3072 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.60 % Allowed : 2.98 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.14), residues: 2592 helix: 1.04 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -1.85 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 32 TYR 0.016 0.002 TYR C 64 TRP 0.010 0.002 TRP U 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (21972) covalent geometry : angle 0.59957 / 0.32 (29724) hydrogen bonds : bond 0.04723 / 3.13 ( 1764) hydrogen bonds : angle 3.76401 / 2.70 ( 5292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.039 Fit side-chains REVERT: I 32 LEU cc_start: 0.9879 (mt) cc_final: 0.9676 (tp) REVERT: I 37 ASP cc_start: 0.9471 (t0) cc_final: 0.9255 (t0) REVERT: I 42 GLU cc_start: 0.9634 (mt-10) cc_final: 0.9429 (mp0) REVERT: I 108 ASN cc_start: 0.9177 (t0) cc_final: 0.8222 (t0) REVERT: I 110 ASP cc_start: 0.8636 (m-30) cc_final: 0.8230 (p0) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0421 time to fit residues: 1.5011 Evaluate side-chains 22 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.038 Evaluate side-chains 26 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 11 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8533 (mm-30) REVERT: Q 18 GLU cc_start: 0.8794 (tp30) cc_final: 0.8394 (tp30) REVERT: Q 33 ASP cc_start: 0.9129 (t0) cc_final: 0.8807 (t0) REVERT: Q 36 ASN cc_start: 0.8731 (t0) cc_final: 0.8157 (t0) REVERT: Q 38 GLU cc_start: 0.8774 (pm20) cc_final: 0.8534 (pm20) REVERT: Q 52 ASP cc_start: 0.8211 (t0) cc_final: 0.7903 (t0) REVERT: Q 70 ASN cc_start: 0.8746 (t0) cc_final: 0.8370 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0991 time to fit residues: 2.7135 Evaluate side-chains 19 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.031939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.025016 restraints weight = 6983.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.026185 restraints weight = 4620.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.027113 restraints weight = 3332.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.027769 restraints weight = 2526.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028437 restraints weight = 2045.895| |-----------------------------------------------------------------------------| r_work (final): 0.2566 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.032222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.026165 restraints weight = 6594.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.027280 restraints weight = 3483.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.028100 restraints weight = 2215.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.028618 restraints weight = 1543.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.029114 restraints weight = 1183.995| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21972 Z= 0.132 Angle : 0.639 12.109 29724 Z= 0.311 Chirality : 0.045 0.360 2964 Planarity : 0.004 0.029 3888 Dihedral : 3.975 14.709 3072 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.60 % Allowed : 1.79 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.15), residues: 2592 helix: 1.09 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.15 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 32 TYR 0.014 0.001 TYR H 64 TRP 0.012 0.002 TRP O 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21972) covalent geometry : angle 0.63924 / 0.31 (29724) hydrogen bonds : bond 0.04215 / 2.78 ( 1764) hydrogen bonds : angle 3.63351 / 2.61 ( 5292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.035 Fit side-chains revert: symmetry clash REVERT: I 34 LEU cc_start: 0.9259 (mt) cc_final: 0.8929 (mt) REVERT: I 37 ASP cc_start: 0.9448 (t0) cc_final: 0.9078 (t0) REVERT: I 68 LEU cc_start: 0.9750 (pp) cc_final: 0.9330 (mt) REVERT: I 108 ASN cc_start: 0.9266 (t0) cc_final: 0.8292 (t0) REVERT: I 110 ASP cc_start: 0.8874 (m-30) cc_final: 0.8474 (p0) REVERT: I 113 GLU cc_start: 0.9615 (tt0) cc_final: 0.9276 (tm-30) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0334 time to fit residues: 1.2239 Evaluate side-chains 13 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.038 Evaluate side-chains 25 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 23 ILE cc_start: 0.9703 (pt) cc_final: 0.9340 (mt) REVERT: V 33 ASP cc_start: 0.9142 (t0) cc_final: 0.8808 (t0) REVERT: V 36 ASN cc_start: 0.8734 (t0) cc_final: 0.8271 (t0) REVERT: V 38 GLU cc_start: 0.8891 (pm20) cc_final: 0.8685 (pm20) REVERT: V 52 ASP cc_start: 0.8246 (t0) cc_final: 0.7903 (t0) REVERT: V 67 ASP cc_start: 0.9385 (t70) cc_final: 0.9171 (t0) REVERT: V 70 ASN cc_start: 0.8524 (t0) cc_final: 0.7861 (t0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1136 time to fit residues: 2.9674 Evaluate side-chains 20 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 174 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 211 optimal weight: 0.0170 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 154 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.031571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.024333 restraints weight = 6831.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.025378 restraints weight = 4596.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.026119 restraints weight = 3366.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.026740 restraints weight = 2635.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.027369 restraints weight = 2136.984| |-----------------------------------------------------------------------------| r_work (final): 0.2534 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.030700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.025198 restraints weight = 6512.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.026261 restraints weight = 3305.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.026918 restraints weight = 2054.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.027530 restraints weight = 1446.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.027900 restraints weight = 1063.496| |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21972 Z= 0.122 Angle : 0.563 7.468 29724 Z= 0.283 Chirality : 0.040 0.166 2964 Planarity : 0.003 0.030 3888 Dihedral : 3.852 15.281 3072 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.60 % Allowed : 1.79 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.15), residues: 2592 helix: 1.14 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.47 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 19 TYR 0.009 0.001 TYR L 64 TRP 0.012 0.002 TRP U 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (21972) covalent geometry : angle 0.56298 / 0.28 (29724) hydrogen bonds : bond 0.03902 / 2.58 ( 1764) hydrogen bonds : angle 3.52320 / 2.52 ( 5292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: E 34 LEU cc_start: 0.9221 (mt) cc_final: 0.8888 (mt) REVERT: E 37 ASP cc_start: 0.9444 (t0) cc_final: 0.8960 (t0) REVERT: E 68 LEU cc_start: 0.9703 (pp) cc_final: 0.9352 (mt) REVERT: E 108 ASN cc_start: 0.9279 (t0) cc_final: 0.8497 (t0) REVERT: E 110 ASP cc_start: 0.9018 (m-30) cc_final: 0.8670 (p0) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0454 time to fit residues: 1.2964 Evaluate side-chains 14 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.039 Evaluate side-chains 26 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 23 ILE cc_start: 0.9700 (pt) cc_final: 0.9374 (mt) REVERT: N 33 ASP cc_start: 0.9097 (t0) cc_final: 0.8798 (t0) REVERT: N 36 ASN cc_start: 0.8633 (t0) cc_final: 0.8001 (t0) REVERT: N 38 GLU cc_start: 0.9035 (pm20) cc_final: 0.8715 (pm20) REVERT: N 52 ASP cc_start: 0.8302 (t0) cc_final: 0.7994 (t0) REVERT: N 70 ASN cc_start: 0.8664 (t0) cc_final: 0.8099 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0991 time to fit residues: 2.7142 Evaluate side-chains 19 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 94 optimal weight: 0.0170 chunk 58 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 198 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 167 optimal weight: 0.3980 chunk 166 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.032563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.024872 restraints weight = 6777.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.026066 restraints weight = 4582.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.027030 restraints weight = 3331.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.027760 restraints weight = 2542.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028282 restraints weight = 2021.374| |-----------------------------------------------------------------------------| r_work (final): 0.2540 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.029046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.024371 restraints weight = 7017.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.025288 restraints weight = 3325.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.026051 restraints weight = 2035.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.026581 restraints weight = 1359.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.026906 restraints weight = 964.157| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21972 Z= 0.123 Angle : 0.583 6.763 29724 Z= 0.294 Chirality : 0.038 0.114 2964 Planarity : 0.003 0.030 3888 Dihedral : 3.887 16.290 3072 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.60 % Allowed : 1.19 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.15), residues: 2592 helix: 1.13 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.71 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.010 0.001 TYR R 87 TRP 0.010 0.002 TRP U 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (21972) covalent geometry : angle 0.58276 / 0.29 (29724) hydrogen bonds : bond 0.03780 / 2.49 ( 1764) hydrogen bonds : angle 3.54068 / 2.55 ( 5292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 34 LEU cc_start: 0.9156 (mt) cc_final: 0.8818 (mt) REVERT: I 37 ASP cc_start: 0.9450 (t0) cc_final: 0.9099 (t0) REVERT: I 68 LEU cc_start: 0.9761 (pp) cc_final: 0.9456 (mt) REVERT: I 108 ASN cc_start: 0.9461 (t0) cc_final: 0.8637 (t0) REVERT: I 110 ASP cc_start: 0.9083 (m-30) cc_final: 0.8672 (p0) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0424 time to fit residues: 1.2555 Evaluate side-chains 15 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.036 Evaluate side-chains 27 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8870 (tm-30) REVERT: N 15 LYS cc_start: 0.9321 (mmpt) cc_final: 0.8997 (mmmt) REVERT: N 18 GLU cc_start: 0.8939 (tp30) cc_final: 0.8720 (tp30) REVERT: N 23 ILE cc_start: 0.9702 (pt) cc_final: 0.9395 (mt) REVERT: N 36 ASN cc_start: 0.8733 (t0) cc_final: 0.8052 (t0) REVERT: N 38 GLU cc_start: 0.9040 (pm20) cc_final: 0.8682 (pm20) REVERT: N 52 ASP cc_start: 0.8445 (t0) cc_final: 0.8170 (t0) REVERT: N 70 ASN cc_start: 0.8861 (t0) cc_final: 0.8230 (t0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0995 time to fit residues: 2.8195 Evaluate side-chains 21 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 55 optimal weight: 4.9990 chunk 237 optimal weight: 0.0060 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.025870 restraints weight = 6760.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.027184 restraints weight = 4496.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.028182 restraints weight = 3229.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.029078 restraints weight = 2449.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.029635 restraints weight = 1901.649| |-----------------------------------------------------------------------------| r_work (final): 0.2571 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.029496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2323 r_free = 0.2323 target = 0.024077 restraints weight = 6640.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.025115 restraints weight = 3334.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.025885 restraints weight = 2063.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.026444 restraints weight = 1434.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.026824 restraints weight = 1070.003| |-----------------------------------------------------------------------------| r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21972 Z= 0.131 Angle : 0.603 8.969 29724 Z= 0.298 Chirality : 0.039 0.111 2964 Planarity : 0.003 0.029 3888 Dihedral : 4.001 17.261 3072 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.60 % Allowed : 4.17 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 2592 helix: 1.10 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.87 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 19 TYR 0.009 0.001 TYR U 87 TRP 0.015 0.002 TRP S 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21972) covalent geometry : angle 0.60336 / 0.30 (29724) hydrogen bonds : bond 0.03877 / 2.56 ( 1764) hydrogen bonds : angle 3.46597 / 2.49 ( 5292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: E 34 LEU cc_start: 0.9199 (mt) cc_final: 0.8836 (mt) REVERT: E 37 ASP cc_start: 0.9414 (t0) cc_final: 0.8936 (t0) REVERT: E 68 LEU cc_start: 0.9710 (pp) cc_final: 0.9436 (mt) REVERT: E 108 ASN cc_start: 0.9234 (t0) cc_final: 0.8231 (t0) REVERT: E 110 ASP cc_start: 0.8822 (m-30) cc_final: 0.8399 (p0) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0392 time to fit residues: 1.2117 Evaluate side-chains 12 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.037 Evaluate side-chains 24 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8846 (tm-30) REVERT: N 15 LYS cc_start: 0.9271 (mmpt) cc_final: 0.8959 (mmmt) REVERT: N 18 GLU cc_start: 0.8982 (tp30) cc_final: 0.8730 (tp30) REVERT: N 23 ILE cc_start: 0.9704 (pt) cc_final: 0.9413 (mt) REVERT: N 36 ASN cc_start: 0.8761 (t0) cc_final: 0.8088 (t0) REVERT: N 38 GLU cc_start: 0.9044 (pm20) cc_final: 0.8646 (pm20) REVERT: N 52 ASP cc_start: 0.8475 (t0) cc_final: 0.8199 (t0) REVERT: N 70 ASN cc_start: 0.8776 (t0) cc_final: 0.8231 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0860 time to fit residues: 2.1770 Evaluate side-chains 18 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 57 optimal weight: 0.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.032801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.025110 restraints weight = 6777.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.026200 restraints weight = 4718.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.027147 restraints weight = 3528.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.027942 restraints weight = 2742.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.028451 restraints weight = 2174.499| |-----------------------------------------------------------------------------| r_work (final): 0.2562 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.027745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2279 r_free = 0.2279 target = 0.022682 restraints weight = 6913.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.023666 restraints weight = 3511.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.024461 restraints weight = 2191.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.024988 restraints weight = 1466.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.025345 restraints weight = 1068.881| |-----------------------------------------------------------------------------| r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21972 Z= 0.141 Angle : 0.616 6.995 29724 Z= 0.319 Chirality : 0.039 0.103 2964 Planarity : 0.003 0.031 3888 Dihedral : 3.982 13.602 3072 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 2592 helix: 0.93 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -3.98 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 107 TYR 0.006 0.001 TYR S 87 TRP 0.062 0.005 TRP P 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21972) covalent geometry : angle 0.61619 / 0.32 (29724) hydrogen bonds : bond 0.03875 / 2.57 ( 1764) hydrogen bonds : angle 3.78240 / 2.75 ( 5292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: E 34 LEU cc_start: 0.9210 (mt) cc_final: 0.8859 (mt) REVERT: E 37 ASP cc_start: 0.9461 (t0) cc_final: 0.9016 (t0) REVERT: E 68 LEU cc_start: 0.9704 (pp) cc_final: 0.9365 (mt) REVERT: E 108 ASN cc_start: 0.9336 (t0) cc_final: 0.8573 (p0) REVERT: E 110 ASP cc_start: 0.8921 (m-30) cc_final: 0.8598 (p0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0619 time to fit residues: 1.7696 Evaluate side-chains 15 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.038 Evaluate side-chains 23 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8810 (tm-30) REVERT: N 15 LYS cc_start: 0.9268 (mmpt) cc_final: 0.8935 (mmmt) REVERT: N 18 GLU cc_start: 0.8981 (tp30) cc_final: 0.8753 (tp30) REVERT: N 23 ILE cc_start: 0.9698 (pt) cc_final: 0.9399 (mt) REVERT: N 36 ASN cc_start: 0.8786 (t0) cc_final: 0.8087 (t0) REVERT: N 38 GLU cc_start: 0.9016 (pm20) cc_final: 0.8609 (pm20) REVERT: N 52 ASP cc_start: 0.8509 (t0) cc_final: 0.8240 (t0) REVERT: N 67 ASP cc_start: 0.9304 (t0) cc_final: 0.9006 (t0) REVERT: N 70 ASN cc_start: 0.8901 (t0) cc_final: 0.8208 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1059 time to fit residues: 2.5486 Evaluate side-chains 18 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 100 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.025737 restraints weight = 6964.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.026770 restraints weight = 4803.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.027558 restraints weight = 3583.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.028145 restraints weight = 2813.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.028631 restraints weight = 2313.487| |-----------------------------------------------------------------------------| r_work (final): 0.2551 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.027761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.022942 restraints weight = 7203.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.023895 restraints weight = 3527.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.024582 restraints weight = 2131.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.025068 restraints weight = 1441.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.025409 restraints weight = 1052.351| |-----------------------------------------------------------------------------| r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21972 Z= 0.149 Angle : 0.683 6.633 29724 Z= 0.346 Chirality : 0.041 0.145 2964 Planarity : 0.004 0.042 3888 Dihedral : 4.155 14.681 3072 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 2592 helix: 0.80 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -4.06 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 19 TYR 0.007 0.001 TYR O 87 TRP 0.042 0.003 TRP R 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (21972) covalent geometry : angle 0.68329 / 0.35 (29724) hydrogen bonds : bond 0.04003 / 2.63 ( 1764) hydrogen bonds : angle 3.79907 / 2.77 ( 5292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.038 Fit side-chains REVERT: D 34 LEU cc_start: 0.9073 (mt) cc_final: 0.8760 (mt) REVERT: D 37 ASP cc_start: 0.9498 (t0) cc_final: 0.9154 (t0) REVERT: D 42 GLU cc_start: 0.9430 (pm20) cc_final: 0.8799 (pm20) REVERT: D 68 LEU cc_start: 0.9737 (pp) cc_final: 0.9428 (mt) REVERT: D 71 ASP cc_start: 0.9419 (t0) cc_final: 0.9188 (t0) REVERT: D 108 ASN cc_start: 0.9023 (t0) cc_final: 0.8686 (t0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0427 time to fit residues: 1.2222 Evaluate side-chains 15 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.037 Evaluate side-chains 21 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9316 (tm-30) cc_final: 0.8826 (tm-30) REVERT: N 15 LYS cc_start: 0.9291 (mmpt) cc_final: 0.8967 (mmmt) REVERT: N 18 GLU cc_start: 0.9021 (tp30) cc_final: 0.8758 (tp30) REVERT: N 23 ILE cc_start: 0.9698 (pt) cc_final: 0.9393 (mt) REVERT: N 36 ASN cc_start: 0.8744 (t0) cc_final: 0.8043 (t0) REVERT: N 38 GLU cc_start: 0.9004 (pm20) cc_final: 0.8626 (pm20) REVERT: N 52 ASP cc_start: 0.8499 (t0) cc_final: 0.8244 (t0) REVERT: N 70 ASN cc_start: 0.8686 (t0) cc_final: 0.8235 (t0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1044 time to fit residues: 2.3024 Evaluate side-chains 16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 159 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 chunk 68 optimal weight: 0.2980 chunk 110 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.1950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.034354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.026221 restraints weight = 6518.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.027271 restraints weight = 4566.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.028110 restraints weight = 3467.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028857 restraints weight = 2775.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.029470 restraints weight = 2249.863| |-----------------------------------------------------------------------------| r_work (final): 0.2565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.028111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.023075 restraints weight = 6786.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.024041 restraints weight = 3387.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.024723 restraints weight = 2062.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.025227 restraints weight = 1411.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.025582 restraints weight = 1046.666| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21972 Z= 0.135 Angle : 0.660 7.490 29724 Z= 0.340 Chirality : 0.040 0.162 2964 Planarity : 0.004 0.043 3888 Dihedral : 4.105 13.568 3072 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 2592 helix: 0.78 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -4.17 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 19 TYR 0.008 0.001 TYR G 64 TRP 0.030 0.003 TRP X 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (21972) covalent geometry : angle 0.65963 / 0.34 (29724) hydrogen bonds : bond 0.04020 / 2.66 ( 1764) hydrogen bonds : angle 3.71898 / 2.71 ( 5292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: I 34 LEU cc_start: 0.9166 (mt) cc_final: 0.8878 (mt) REVERT: I 37 ASP cc_start: 0.9420 (t0) cc_final: 0.9053 (t0) REVERT: I 42 GLU cc_start: 0.9444 (pm20) cc_final: 0.8911 (pm20) REVERT: I 68 LEU cc_start: 0.9730 (pp) cc_final: 0.9448 (mt) REVERT: I 71 ASP cc_start: 0.9485 (t0) cc_final: 0.9275 (t0) REVERT: I 108 ASN cc_start: 0.9050 (t0) cc_final: 0.8640 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0450 time to fit residues: 1.3322 Evaluate side-chains 17 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.046 Evaluate side-chains 25 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8785 (tm-30) REVERT: N 15 LYS cc_start: 0.9286 (mmpt) cc_final: 0.8977 (mmmt) REVERT: N 18 GLU cc_start: 0.9015 (tp30) cc_final: 0.8699 (tp30) REVERT: N 23 ILE cc_start: 0.9678 (pt) cc_final: 0.9377 (mt) REVERT: N 36 ASN cc_start: 0.8733 (t0) cc_final: 0.7979 (t0) REVERT: N 38 GLU cc_start: 0.8983 (pm20) cc_final: 0.8553 (pm20) REVERT: N 52 ASP cc_start: 0.8478 (t0) cc_final: 0.8226 (t0) REVERT: N 70 ASN cc_start: 0.8693 (t0) cc_final: 0.8231 (t0) REVERT: N 99 GLU cc_start: 0.8268 (pp20) cc_final: 0.8062 (mp0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1032 time to fit residues: 2.7104 Evaluate side-chains 19 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.033145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.025917 restraints weight = 6888.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.026965 restraints weight = 4775.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.027788 restraints weight = 3573.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.028366 restraints weight = 2808.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.028946 restraints weight = 2323.646| |-----------------------------------------------------------------------------| r_work (final): 0.2553 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.029755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.023619 restraints weight = 6535.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.024720 restraints weight = 3261.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.025462 restraints weight = 2028.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.026054 restraints weight = 1435.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.026469 restraints weight = 1102.020| |-----------------------------------------------------------------------------| r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21972 Z= 0.144 Angle : 0.648 7.233 29724 Z= 0.330 Chirality : 0.040 0.129 2964 Planarity : 0.004 0.035 3888 Dihedral : 4.198 19.560 3072 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2592 helix: 1.05 (0.10), residues: 2412 sheet: None (None), residues: 0 loop : -3.90 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 19 TYR 0.008 0.001 TYR M 30 TRP 0.027 0.003 TRP X 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21972) covalent geometry : angle 0.64812 / 0.33 (29724) hydrogen bonds : bond 0.03822 / 2.53 ( 1764) hydrogen bonds : angle 3.85866 / 2.80 ( 5292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 LEU cc_start: 0.9042 (mt) cc_final: 0.8720 (mt) REVERT: D 37 ASP cc_start: 0.9473 (t0) cc_final: 0.9127 (t0) REVERT: D 42 GLU cc_start: 0.9418 (pm20) cc_final: 0.8793 (pm20) REVERT: D 68 LEU cc_start: 0.9745 (pp) cc_final: 0.9482 (mt) REVERT: D 108 ASN cc_start: 0.9007 (t0) cc_final: 0.8507 (t0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0385 time to fit residues: 1.0997 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.061 Evaluate side-chains 24 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 11 GLU cc_start: 0.9317 (tm-30) cc_final: 0.8810 (tm-30) REVERT: V 15 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8751 (mmmt) REVERT: V 18 GLU cc_start: 0.9146 (tp30) cc_final: 0.8671 (tp30) REVERT: V 23 ILE cc_start: 0.9734 (pt) cc_final: 0.9366 (mt) REVERT: V 36 ASN cc_start: 0.8830 (t0) cc_final: 0.8105 (t0) REVERT: V 38 GLU cc_start: 0.8967 (pm20) cc_final: 0.8652 (pm20) REVERT: V 52 ASP cc_start: 0.8357 (t0) cc_final: 0.8055 (t0) REVERT: V 58 ARG cc_start: 0.9729 (mtp180) cc_final: 0.9059 (ptm160) REVERT: V 70 ASN cc_start: 0.8579 (t0) cc_final: 0.8171 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1144 time to fit residues: 2.8702 Evaluate side-chains 20 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 161 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 GLN V 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.026388 restraints weight = 6794.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.027513 restraints weight = 4702.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.028407 restraints weight = 3497.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.029142 restraints weight = 2730.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.029655 restraints weight = 2196.763| |-----------------------------------------------------------------------------| r_work (final): 0.2546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.029394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.023524 restraints weight = 6505.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.024604 restraints weight = 3273.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.025378 restraints weight = 2030.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.025919 restraints weight = 1418.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.026308 restraints weight = 1073.935| |-----------------------------------------------------------------------------| r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21972 Z= 0.133 Angle : 0.622 7.023 29724 Z= 0.315 Chirality : 0.039 0.107 2964 Planarity : 0.004 0.034 3888 Dihedral : 4.178 17.626 3072 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.16), residues: 2592 helix: 1.04 (0.10), residues: 2412 sheet: None (None), residues: 0 loop : -4.05 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 19 TYR 0.008 0.001 TYR M 30 TRP 0.025 0.003 TRP X 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21972) covalent geometry : angle 0.62208 / 0.32 (29724) hydrogen bonds : bond 0.03842 / 2.53 ( 1764) hydrogen bonds : angle 3.79232 / 2.75 ( 5292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1665.87 seconds wall clock time: 31 minutes 1.88 seconds (1861.88 seconds total)