Starting phenix.real_space_refine on Thu Mar 5 09:42:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vl6_21231/03_2026/6vl6_21231.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vl6_21231/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vl6_21231/03_2026/6vl6_21231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vl6_21231/03_2026/6vl6_21231.map" model { file = "/net/cci-nas-00/data/ceres_data/6vl6_21231/03_2026/6vl6_21231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vl6_21231/03_2026/6vl6_21231.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.03, per 1000 atoms: 0.09 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: 2.01 Conformation dependent library (CDL) restraints added in 924.9 milliseconds 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: 0.61 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: 3.72 Time building geometry restraints manager: 2.63 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: 0.07 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: 7.650 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: 16.720 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 covalent geometry : bond 0.01867 (21972) covalent geometry : angle 1.45581 (29724) hydrogen bonds : bond 0.13473 ( 1764) hydrogen bonds : angle 5.34972 ( 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 : 0.028 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: 0.1046 time to fit residues: 4.1769 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 : 0.038 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 : 0.031 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: 0.1450 time to fit residues: 4.6449 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 : 0.029 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2736 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 = 0.2689 r_free = 0.2689 target = 0.033081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.026784 restraints weight = 6047.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.027914 restraints weight = 3437.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028833 restraints weight = 2292.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.029465 restraints weight = 1614.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.029833 restraints weight = 1215.001| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4253 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 covalent geometry : bond 0.00311 (21972) covalent geometry : angle 0.59957 (29724) hydrogen bonds : bond 0.04723 ( 1764) hydrogen bonds : angle 3.76401 ( 5292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 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 : 0.036 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: 0.0316 time to fit residues: 1.1225 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 : 0.041 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 : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 11 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8528 (mm-30) REVERT: Q 18 GLU cc_start: 0.8794 (tp30) cc_final: 0.8395 (tp30) REVERT: Q 33 ASP cc_start: 0.9121 (t0) cc_final: 0.8803 (t0) REVERT: Q 36 ASN cc_start: 0.8726 (t0) cc_final: 0.8149 (t0) REVERT: Q 38 GLU cc_start: 0.8762 (pm20) cc_final: 0.8525 (pm20) REVERT: Q 52 ASP cc_start: 0.8208 (t0) cc_final: 0.7900 (t0) REVERT: Q 70 ASN cc_start: 0.8728 (t0) cc_final: 0.8358 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1100 time to fit residues: 3.0242 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 157 optimal weight: 0.0980 chunk 176 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 overall best weight: 0.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.032176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.024569 restraints weight = 6959.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.025711 restraints weight = 4600.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.026704 restraints weight = 3348.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.027418 restraints weight = 2562.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.028035 restraints weight = 2062.821| |-----------------------------------------------------------------------------| r_work (final): 0.2579 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.025814 restraints weight = 6722.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.026927 restraints weight = 3531.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.027714 restraints weight = 2211.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.028254 restraints weight = 1544.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.028734 restraints weight = 1172.046| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21972 Z= 0.147 Angle : 0.735 15.250 29724 Z= 0.348 Chirality : 0.044 0.292 2964 Planarity : 0.004 0.030 3888 Dihedral : 4.047 15.333 3072 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.19 % Allowed : 1.79 % Favored : 97.02 % 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: 0.65 (0.15), residues: 2592 helix: 0.70 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.38 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.028 0.002 TYR I 57 TRP 0.013 0.002 TRP U 74 Details of bonding type rmsd covalent geometry : bond 0.00315 (21972) covalent geometry : angle 0.73501 (29724) hydrogen bonds : bond 0.04239 ( 1764) hydrogen bonds : angle 3.71499 ( 5292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 6 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8752 (pp) REVERT: I 10 MET cc_start: 0.9465 (mmp) cc_final: 0.8665 (mtp) REVERT: I 34 LEU cc_start: 0.9286 (mt) cc_final: 0.8984 (mt) REVERT: I 37 ASP cc_start: 0.9484 (t0) cc_final: 0.9145 (t0) REVERT: I 58 ASP cc_start: 0.9571 (p0) cc_final: 0.9162 (p0) REVERT: I 68 LEU cc_start: 0.9749 (pp) cc_final: 0.9380 (mt) REVERT: I 92 ASP cc_start: 0.9395 (p0) cc_final: 0.9167 (p0) REVERT: I 108 ASN cc_start: 0.9325 (t0) cc_final: 0.8318 (t0) REVERT: I 110 ASP cc_start: 0.8841 (m-30) cc_final: 0.8360 (p0) REVERT: I 112 ILE cc_start: 0.9856 (mt) cc_final: 0.9574 (mm) REVERT: I 113 GLU cc_start: 0.9568 (tt0) cc_final: 0.9120 (tm-30) REVERT: I 116 ILE cc_start: 0.9747 (OUTLIER) cc_final: 0.9544 (tp) outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.0420 time to fit residues: 1.5736 Evaluate side-chains 28 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.038 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 : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 23 ILE cc_start: 0.9709 (pt) cc_final: 0.9414 (mt) REVERT: N 33 ASP cc_start: 0.9068 (t0) cc_final: 0.8740 (t0) REVERT: N 36 ASN cc_start: 0.8594 (t0) cc_final: 0.8004 (t0) REVERT: N 38 GLU cc_start: 0.8878 (pm20) cc_final: 0.8518 (pm20) REVERT: N 52 ASP cc_start: 0.8272 (t0) cc_final: 0.7968 (t0) REVERT: N 67 ASP cc_start: 0.9326 (t70) cc_final: 0.9119 (t0) REVERT: N 70 ASN cc_start: 0.8780 (t0) cc_final: 0.8112 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1068 time to fit residues: 2.6919 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 : 0.031 ------------------------------------------------------------------------------- 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: 0.0870 chunk 54 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 60 optimal weight: 0.2980 chunk 116 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.031785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.024468 restraints weight = 6813.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.025551 restraints weight = 4413.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.026381 restraints weight = 3174.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.026961 restraints weight = 2428.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027481 restraints weight = 1972.972| |-----------------------------------------------------------------------------| r_work (final): 0.2525 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.031159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.025690 restraints weight = 6720.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.026800 restraints weight = 3528.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.027537 restraints weight = 2198.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.028183 restraints weight = 1547.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.028633 restraints weight = 1138.606| |-----------------------------------------------------------------------------| r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21972 Z= 0.134 Angle : 0.632 11.342 29724 Z= 0.313 Chirality : 0.038 0.129 2964 Planarity : 0.004 0.031 3888 Dihedral : 3.989 15.127 3072 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.45 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: 0.66 (0.15), residues: 2592 helix: 0.72 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.66 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.010 0.001 TYR F 64 TRP 0.021 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00289 (21972) covalent geometry : angle 0.63182 (29724) hydrogen bonds : bond 0.04162 ( 1764) hydrogen bonds : angle 3.71369 ( 5292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 MET cc_start: 0.9482 (mmp) cc_final: 0.8696 (mtp) REVERT: E 34 LEU cc_start: 0.9289 (mt) cc_final: 0.9022 (mt) REVERT: E 37 ASP cc_start: 0.9388 (t0) cc_final: 0.8938 (t0) REVERT: E 58 ASP cc_start: 0.9564 (p0) cc_final: 0.9266 (p0) REVERT: E 68 LEU cc_start: 0.9691 (pp) cc_final: 0.9260 (mt) REVERT: E 108 ASN cc_start: 0.9191 (t0) cc_final: 0.8262 (t0) REVERT: E 110 ASP cc_start: 0.8841 (m-30) cc_final: 0.8292 (p0) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0431 time to fit residues: 1.4694 Evaluate side-chains 21 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.036 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: N 23 ILE cc_start: 0.9704 (pt) cc_final: 0.9376 (mt) REVERT: N 33 ASP cc_start: 0.9006 (t0) cc_final: 0.8677 (t0) REVERT: N 36 ASN cc_start: 0.8555 (t0) cc_final: 0.7963 (t0) REVERT: N 38 GLU cc_start: 0.8945 (pm20) cc_final: 0.8529 (pm20) REVERT: N 52 ASP cc_start: 0.8314 (t0) cc_final: 0.8013 (t0) REVERT: N 70 ASN cc_start: 0.8546 (t0) cc_final: 0.7948 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1083 time to fit residues: 2.7225 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 : 0.031 ------------------------------------------------------------------------------- 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: 9.9990 chunk 105 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 167 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.031967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.024179 restraints weight = 6950.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.025250 restraints weight = 4710.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.026092 restraints weight = 3492.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.026765 restraints weight = 2734.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027396 restraints weight = 2238.592| |-----------------------------------------------------------------------------| r_work (final): 0.2565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.030281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.024746 restraints weight = 7089.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.025768 restraints weight = 3805.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.026521 restraints weight = 2444.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.027022 restraints weight = 1732.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.027483 restraints weight = 1332.969| |-----------------------------------------------------------------------------| r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21972 Z= 0.189 Angle : 0.728 8.063 29724 Z= 0.374 Chirality : 0.041 0.134 2964 Planarity : 0.004 0.030 3888 Dihedral : 4.039 14.433 3072 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.60 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: 0.19 (0.15), residues: 2592 helix: 0.42 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.89 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.016 0.001 TYR O 7 TRP 0.018 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00447 (21972) covalent geometry : angle 0.72772 (29724) hydrogen bonds : bond 0.04179 ( 1764) hydrogen bonds : angle 3.97624 ( 5292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 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 : 0.044 Fit side-chains REVERT: I 10 MET cc_start: 0.9528 (mmp) cc_final: 0.9279 (mmp) REVERT: I 34 LEU cc_start: 0.9289 (mt) cc_final: 0.8955 (mt) REVERT: I 37 ASP cc_start: 0.9456 (t0) cc_final: 0.9084 (t0) REVERT: I 58 ASP cc_start: 0.9577 (p0) cc_final: 0.9217 (p0) REVERT: I 68 LEU cc_start: 0.9764 (pp) cc_final: 0.9420 (mt) REVERT: I 70 LEU cc_start: 0.9525 (tp) cc_final: 0.9185 (tt) REVERT: I 108 ASN cc_start: 0.9402 (t0) cc_final: 0.8538 (p0) REVERT: I 110 ASP cc_start: 0.8936 (m-30) cc_final: 0.8530 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0266 time to fit residues: 0.8223 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 : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 15 LYS cc_start: 0.9475 (mmpt) cc_final: 0.8926 (mmmt) REVERT: N 23 ILE cc_start: 0.9714 (pt) cc_final: 0.9407 (mt) REVERT: N 33 ASP cc_start: 0.9016 (t0) cc_final: 0.8660 (t0) REVERT: N 36 ASN cc_start: 0.8603 (t0) cc_final: 0.7967 (t0) REVERT: N 38 GLU cc_start: 0.8857 (pm20) cc_final: 0.8536 (pm20) REVERT: N 52 ASP cc_start: 0.8379 (t0) cc_final: 0.8079 (t0) REVERT: N 70 ASN cc_start: 0.8612 (t0) cc_final: 0.7938 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0914 time to fit residues: 2.3068 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 : 0.029 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 100.0000 chunk 129 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.032434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.024861 restraints weight = 7000.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.026012 restraints weight = 4495.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.026908 restraints weight = 3211.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027597 restraints weight = 2429.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.028197 restraints weight = 1918.774| |-----------------------------------------------------------------------------| r_work (final): 0.2544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.030779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.025027 restraints weight = 6543.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.026098 restraints weight = 3466.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.026859 restraints weight = 2200.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.027422 restraints weight = 1556.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.027884 restraints weight = 1182.050| |-----------------------------------------------------------------------------| r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21972 Z= 0.189 Angle : 0.728 8.062 29724 Z= 0.373 Chirality : 0.041 0.134 2964 Planarity : 0.004 0.030 3888 Dihedral : 4.039 14.433 3072 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.15), residues: 2592 helix: 0.42 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.89 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 19 TYR 0.016 0.001 TYR R 7 TRP 0.018 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00446 (21972) covalent geometry : angle 0.72761 (29724) hydrogen bonds : bond 0.04179 ( 1764) hydrogen bonds : angle 3.97625 ( 5292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.038 Fit side-chains REVERT: E 34 LEU cc_start: 0.9269 (mt) cc_final: 0.8955 (mt) REVERT: E 37 ASP cc_start: 0.9390 (t0) cc_final: 0.8936 (t0) REVERT: E 58 ASP cc_start: 0.9657 (p0) cc_final: 0.9341 (p0) REVERT: E 68 LEU cc_start: 0.9687 (pp) cc_final: 0.9256 (mt) REVERT: E 70 LEU cc_start: 0.9414 (tp) cc_final: 0.9092 (tt) REVERT: E 108 ASN cc_start: 0.9196 (t0) cc_final: 0.8260 (p0) REVERT: E 110 ASP cc_start: 0.8809 (m-30) cc_final: 0.8365 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0358 time to fit residues: 0.9735 Evaluate side-chains 11 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.037 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 : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 15 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8929 (mmmt) REVERT: N 23 ILE cc_start: 0.9713 (pt) cc_final: 0.9398 (mt) REVERT: N 33 ASP cc_start: 0.8996 (t0) cc_final: 0.8643 (t0) REVERT: N 36 ASN cc_start: 0.8571 (t0) cc_final: 0.7937 (t0) REVERT: N 38 GLU cc_start: 0.8873 (pm20) cc_final: 0.8545 (pm20) REVERT: N 52 ASP cc_start: 0.8337 (t0) cc_final: 0.8038 (t0) REVERT: N 70 ASN cc_start: 0.8515 (t0) cc_final: 0.7941 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0957 time to fit residues: 2.3223 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 : 0.030 ------------------------------------------------------------------------------- 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: 0.5980 chunk 164 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.031984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.024849 restraints weight = 7067.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.026128 restraints weight = 4275.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.027103 restraints weight = 2922.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027766 restraints weight = 2146.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.028371 restraints weight = 1685.388| |-----------------------------------------------------------------------------| r_work (final): 0.2582 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.030735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.024978 restraints weight = 6697.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.026069 restraints weight = 3523.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.026838 restraints weight = 2214.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.027271 restraints weight = 1553.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.027797 restraints weight = 1211.493| |-----------------------------------------------------------------------------| r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21972 Z= 0.199 Angle : 0.752 10.885 29724 Z= 0.378 Chirality : 0.041 0.136 2964 Planarity : 0.004 0.029 3888 Dihedral : 4.098 15.588 3072 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.61 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: 0.18 (0.15), residues: 2592 helix: 0.41 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 19 TYR 0.010 0.001 TYR F 64 TRP 0.016 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00485 (21972) covalent geometry : angle 0.75194 (29724) hydrogen bonds : bond 0.04097 ( 1764) hydrogen bonds : angle 3.97142 ( 5292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 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 : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 LEU cc_start: 0.9227 (mt) cc_final: 0.8924 (mt) REVERT: H 37 ASP cc_start: 0.9395 (t0) cc_final: 0.9098 (t0) REVERT: H 58 ASP cc_start: 0.9576 (p0) cc_final: 0.9251 (p0) REVERT: H 68 LEU cc_start: 0.9743 (pp) cc_final: 0.9394 (mt) REVERT: H 70 LEU cc_start: 0.9462 (tp) cc_final: 0.9182 (tt) REVERT: H 113 GLU cc_start: 0.9506 (tt0) cc_final: 0.9217 (tm-30) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0408 time to fit residues: 1.1518 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 23 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8899 (tm-30) REVERT: N 23 ILE cc_start: 0.9707 (pt) cc_final: 0.9384 (mt) REVERT: N 33 ASP cc_start: 0.8988 (t0) cc_final: 0.8636 (t0) REVERT: N 36 ASN cc_start: 0.8585 (t0) cc_final: 0.7969 (t0) REVERT: N 38 GLU cc_start: 0.8917 (pm20) cc_final: 0.8579 (pm20) REVERT: N 52 ASP cc_start: 0.8332 (t0) cc_final: 0.8037 (t0) REVERT: N 70 ASN cc_start: 0.8517 (t0) cc_final: 0.7896 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1085 time to fit residues: 2.6213 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 : 0.030 ------------------------------------------------------------------------------- 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: 0.0670 chunk 169 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 239 optimal weight: 0.0170 chunk 154 optimal weight: 2.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.031196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.023832 restraints weight = 6783.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.024879 restraints weight = 4486.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.025717 restraints weight = 3263.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.026390 restraints weight = 2514.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.026858 restraints weight = 2002.730| |-----------------------------------------------------------------------------| r_work (final): 0.2526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.030125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.024761 restraints weight = 6605.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.025826 restraints weight = 3535.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.026516 restraints weight = 2239.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.027193 restraints weight = 1597.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.027670 restraints weight = 1181.213| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21972 Z= 0.199 Angle : 0.752 10.872 29724 Z= 0.378 Chirality : 0.041 0.135 2964 Planarity : 0.004 0.029 3888 Dihedral : 4.098 15.588 3072 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.15), residues: 2592 helix: 0.41 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.010 0.001 TYR D 64 TRP 0.016 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00484 (21972) covalent geometry : angle 0.75164 (29724) hydrogen bonds : bond 0.04097 ( 1764) hydrogen bonds : angle 3.97161 ( 5292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 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: E 34 LEU cc_start: 0.9300 (mt) cc_final: 0.8986 (mt) REVERT: E 37 ASP cc_start: 0.9416 (t0) cc_final: 0.8971 (t0) REVERT: E 42 GLU cc_start: 0.9506 (mp0) cc_final: 0.9282 (mp0) REVERT: E 58 ASP cc_start: 0.9633 (p0) cc_final: 0.9259 (p0) REVERT: E 68 LEU cc_start: 0.9697 (pp) cc_final: 0.9318 (mt) REVERT: E 70 LEU cc_start: 0.9430 (tp) cc_final: 0.9062 (tt) REVERT: E 108 ASN cc_start: 0.9316 (t0) cc_final: 0.8429 (p0) REVERT: E 110 ASP cc_start: 0.8916 (m-30) cc_final: 0.8346 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0430 time to fit residues: 1.2128 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 : 0.038 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 : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8867 (tm-30) REVERT: N 23 ILE cc_start: 0.9713 (pt) cc_final: 0.9400 (mt) REVERT: N 33 ASP cc_start: 0.9059 (t0) cc_final: 0.8702 (t0) REVERT: N 36 ASN cc_start: 0.8641 (t0) cc_final: 0.8003 (t0) REVERT: N 38 GLU cc_start: 0.8876 (pm20) cc_final: 0.8541 (pm20) REVERT: N 52 ASP cc_start: 0.8373 (t0) cc_final: 0.8075 (t0) REVERT: N 70 ASN cc_start: 0.8643 (t0) cc_final: 0.7962 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1046 time to fit residues: 2.5259 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 : 0.036 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 48 optimal weight: 0.0020 chunk 159 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.031686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.024692 restraints weight = 7191.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.025949 restraints weight = 4334.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.026830 restraints weight = 2963.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027602 restraints weight = 2205.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028184 restraints weight = 1698.239| |-----------------------------------------------------------------------------| r_work (final): 0.2590 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.030125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.024792 restraints weight = 6465.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.025843 restraints weight = 3484.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.026603 restraints weight = 2219.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.027218 restraints weight = 1562.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.027673 restraints weight = 1160.577| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21972 Z= 0.199 Angle : 0.752 10.872 29724 Z= 0.378 Chirality : 0.041 0.135 2964 Planarity : 0.004 0.029 3888 Dihedral : 4.098 15.588 3072 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.15), residues: 2592 helix: 0.41 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.010 0.001 TYR K 64 TRP 0.016 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00484 (21972) covalent geometry : angle 0.75164 (29724) hydrogen bonds : bond 0.04097 ( 1764) hydrogen bonds : angle 3.97161 ( 5292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 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 : 0.040 Fit side-chains revert: symmetry clash REVERT: H 34 LEU cc_start: 0.9224 (mt) cc_final: 0.8924 (mt) REVERT: H 37 ASP cc_start: 0.9398 (t0) cc_final: 0.9098 (t0) REVERT: H 58 ASP cc_start: 0.9590 (p0) cc_final: 0.9278 (p0) REVERT: H 68 LEU cc_start: 0.9742 (pp) cc_final: 0.9388 (mt) REVERT: H 70 LEU cc_start: 0.9457 (tp) cc_final: 0.9180 (tt) REVERT: H 108 ASN cc_start: 0.9377 (t0) cc_final: 0.8490 (p0) REVERT: H 110 ASP cc_start: 0.9081 (m-30) cc_final: 0.8502 (p0) REVERT: H 113 GLU cc_start: 0.9534 (tt0) cc_final: 0.9237 (tm-30) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0505 time to fit residues: 1.4206 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 23 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8865 (tm-30) REVERT: N 23 ILE cc_start: 0.9712 (pt) cc_final: 0.9397 (mt) REVERT: N 33 ASP cc_start: 0.9057 (t0) cc_final: 0.8700 (t0) REVERT: N 36 ASN cc_start: 0.8636 (t0) cc_final: 0.7999 (t0) REVERT: N 38 GLU cc_start: 0.8874 (pm20) cc_final: 0.8538 (pm20) REVERT: N 52 ASP cc_start: 0.8377 (t0) cc_final: 0.8079 (t0) REVERT: N 70 ASN cc_start: 0.8634 (t0) cc_final: 0.7955 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1003 time to fit residues: 2.4286 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 : 0.030 ------------------------------------------------------------------------------- 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: 4.9990 chunk 158 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.031212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.023832 restraints weight = 6878.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.024786 restraints weight = 4521.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.025677 restraints weight = 3347.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.026335 restraints weight = 2571.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.026821 restraints weight = 2048.694| |-----------------------------------------------------------------------------| r_work (final): 0.2523 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.030125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.024740 restraints weight = 6658.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.025810 restraints weight = 3569.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.026505 restraints weight = 2253.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.027217 restraints weight = 1602.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.027653 restraints weight = 1163.290| |-----------------------------------------------------------------------------| r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21972 Z= 0.199 Angle : 0.752 10.872 29724 Z= 0.378 Chirality : 0.041 0.135 2964 Planarity : 0.004 0.029 3888 Dihedral : 4.098 15.588 3072 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.15), residues: 2592 helix: 0.41 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 19 TYR 0.010 0.001 TYR M 64 TRP 0.016 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00484 (21972) covalent geometry : angle 0.75163 (29724) hydrogen bonds : bond 0.04097 ( 1764) hydrogen bonds : angle 3.97161 ( 5292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 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 : 0.037 Fit side-chains REVERT: E 34 LEU cc_start: 0.9301 (mt) cc_final: 0.8987 (mt) REVERT: E 37 ASP cc_start: 0.9415 (t0) cc_final: 0.8968 (t0) REVERT: E 42 GLU cc_start: 0.9519 (mp0) cc_final: 0.9297 (mp0) REVERT: E 58 ASP cc_start: 0.9638 (p0) cc_final: 0.9271 (p0) REVERT: E 68 LEU cc_start: 0.9698 (pp) cc_final: 0.9314 (mt) REVERT: E 70 LEU cc_start: 0.9425 (tp) cc_final: 0.9062 (tt) REVERT: E 108 ASN cc_start: 0.9307 (t0) cc_final: 0.8417 (p0) REVERT: E 110 ASP cc_start: 0.8914 (m-30) cc_final: 0.8348 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0481 time to fit residues: 1.3622 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 : 0.036 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 : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8864 (tm-30) REVERT: N 23 ILE cc_start: 0.9712 (pt) cc_final: 0.9398 (mt) REVERT: N 33 ASP cc_start: 0.9058 (t0) cc_final: 0.8701 (t0) REVERT: N 36 ASN cc_start: 0.8637 (t0) cc_final: 0.8000 (t0) REVERT: N 38 GLU cc_start: 0.8873 (pm20) cc_final: 0.8538 (pm20) REVERT: N 52 ASP cc_start: 0.8372 (t0) cc_final: 0.8074 (t0) REVERT: N 70 ASN cc_start: 0.8635 (t0) cc_final: 0.7956 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1091 time to fit residues: 2.6325 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 : 0.019 ------------------------------------------------------------------------------- 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: 0.1980 chunk 222 optimal weight: 0.7980 chunk 132 optimal weight: 0.0070 chunk 85 optimal weight: 0.1980 chunk 244 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 183 optimal weight: 5.9990 chunk 218 optimal weight: 0.0010 chunk 151 optimal weight: 0.0070 chunk 226 optimal weight: 4.9990 overall best weight: 0.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.032016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.024464 restraints weight = 7075.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.025593 restraints weight = 4547.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.026372 restraints weight = 3244.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027110 restraints weight = 2508.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.027612 restraints weight = 1985.297| |-----------------------------------------------------------------------------| r_work (final): 0.2526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.030125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.024746 restraints weight = 6664.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.025813 restraints weight = 3559.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.026508 restraints weight = 2249.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.027230 restraints weight = 1600.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.027653 restraints weight = 1162.914| |-----------------------------------------------------------------------------| r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21972 Z= 0.199 Angle : 0.752 10.871 29724 Z= 0.378 Chirality : 0.041 0.135 2964 Planarity : 0.004 0.029 3888 Dihedral : 4.098 15.588 3072 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.15), residues: 2592 helix: 0.41 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.010 0.001 TYR G 64 TRP 0.016 0.002 TRP R 74 Details of bonding type rmsd covalent geometry : bond 0.00484 (21972) covalent geometry : angle 0.75162 (29724) hydrogen bonds : bond 0.04097 ( 1764) hydrogen bonds : angle 3.97162 ( 5292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.56 seconds wall clock time: 27 minutes 50.92 seconds (1670.92 seconds total)