Starting phenix.real_space_refine on Sat Mar 7 01:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vfh_21172/03_2026/6vfh_21172.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vfh_21172/03_2026/6vfh_21172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vfh_21172/03_2026/6vfh_21172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vfh_21172/03_2026/6vfh_21172.map" model { file = "/net/cci-nas-00/data/ceres_data/6vfh_21172/03_2026/6vfh_21172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vfh_21172/03_2026/6vfh_21172.cif" } resolution = 3.86 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= 0.005 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 120 5.16 5 C 23556 2.51 5 N 6144 2.21 5 O 7164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s 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: 36984 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 3.84, per 1000 atoms: 0.10 Number of scatterers: 36984 At special positions: 0 Unit cell: (180.25, 179.22, 174.07, 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 120 16.00 O 7164 8.00 N 6144 7.00 C 23556 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 104 through 118 Processing helix chain 'B' and resid 2 through 29 Processing helix chain 'B' and resid 32 through 59 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 97 through 121 Processing helix chain 'B' and resid 125 through 152 Processing helix chain 'B' and resid 159 through 183 Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 250 through 277 Processing helix chain 'C' and resid 1 through 16 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 104 through 118 Processing helix chain 'D' and resid 2 through 29 Processing helix chain 'D' and resid 32 through 59 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 97 through 121 Processing helix chain 'D' and resid 125 through 152 Processing helix chain 'D' and resid 159 through 183 Processing helix chain 'D' and resid 187 through 214 Processing helix chain 'D' and resid 218 through 245 Processing helix chain 'D' and resid 250 through 277 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'F' and resid 2 through 29 Processing helix chain 'F' and resid 32 through 59 Processing helix chain 'F' and resid 63 through 89 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 97 through 121 Processing helix chain 'F' and resid 125 through 152 Processing helix chain 'F' and resid 159 through 183 Processing helix chain 'F' and resid 187 through 214 Processing helix chain 'F' and resid 218 through 245 Processing helix chain 'F' and resid 250 through 277 Processing helix chain 'G' and resid 1 through 16 Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 36 through 50 Processing helix chain 'G' and resid 52 through 67 Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 104 through 118 Processing helix chain 'H' and resid 2 through 29 Processing helix chain 'H' and resid 32 through 59 Processing helix chain 'H' and resid 63 through 89 Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 97 through 121 Processing helix chain 'H' and resid 125 through 152 Processing helix chain 'H' and resid 159 through 183 Processing helix chain 'H' and resid 187 through 214 Processing helix chain 'H' and resid 218 through 245 Processing helix chain 'H' and resid 250 through 277 Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 33 Processing helix chain 'I' and resid 36 through 50 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 86 through 101 Processing helix chain 'I' and resid 104 through 118 Processing helix chain 'J' and resid 2 through 29 Processing helix chain 'J' and resid 32 through 59 Processing helix chain 'J' and resid 63 through 89 Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 97 through 121 Processing helix chain 'J' and resid 125 through 152 Processing helix chain 'J' and resid 159 through 183 Processing helix chain 'J' and resid 187 through 214 Processing helix chain 'J' and resid 218 through 245 Processing helix chain 'J' and resid 250 through 277 Processing helix chain 'K' and resid 1 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 67 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 86 through 101 Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'L' and resid 2 through 29 Processing helix chain 'L' and resid 32 through 59 Processing helix chain 'L' and resid 63 through 89 Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 97 through 121 Processing helix chain 'L' and resid 125 through 152 Processing helix chain 'L' and resid 159 through 183 Processing helix chain 'L' and resid 187 through 214 Processing helix chain 'L' and resid 218 through 245 Processing helix chain 'L' and resid 250 through 277 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 36 through 50 Processing helix chain 'M' and resid 52 through 67 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 86 through 101 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'N' and resid 2 through 29 Processing helix chain 'N' and resid 32 through 59 Processing helix chain 'N' and resid 63 through 89 Processing helix chain 'N' and resid 91 through 95 Processing helix chain 'N' and resid 97 through 121 Processing helix chain 'N' and resid 125 through 152 Processing helix chain 'N' and resid 159 through 183 Processing helix chain 'N' and resid 187 through 214 Processing helix chain 'N' and resid 218 through 245 Processing helix chain 'N' and resid 250 through 277 Processing helix chain 'O' and resid 1 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 101 Processing helix chain 'O' and resid 104 through 118 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'P' and resid 32 through 59 Processing helix chain 'P' and resid 63 through 89 Processing helix chain 'P' and resid 91 through 95 Processing helix chain 'P' and resid 97 through 121 Processing helix chain 'P' and resid 125 through 152 Processing helix chain 'P' and resid 159 through 183 Processing helix chain 'P' and resid 187 through 214 Processing helix chain 'P' and resid 218 through 245 Processing helix chain 'P' and resid 250 through 277 Processing helix chain 'Q' and resid 1 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 101 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'R' and resid 2 through 29 Processing helix chain 'R' and resid 32 through 59 Processing helix chain 'R' and resid 63 through 89 Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 97 through 121 Processing helix chain 'R' and resid 125 through 152 Processing helix chain 'R' and resid 159 through 183 Processing helix chain 'R' and resid 187 through 214 Processing helix chain 'R' and resid 218 through 245 Processing helix chain 'R' and resid 250 through 277 Processing helix chain 'S' and resid 1 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 101 Processing helix chain 'S' and resid 104 through 118 Processing helix chain 'T' and resid 2 through 29 Processing helix chain 'T' and resid 32 through 59 Processing helix chain 'T' and resid 63 through 89 Processing helix chain 'T' and resid 91 through 95 Processing helix chain 'T' and resid 97 through 121 Processing helix chain 'T' and resid 125 through 152 Processing helix chain 'T' and resid 159 through 183 Processing helix chain 'T' and resid 187 through 214 Processing helix chain 'T' and resid 218 through 245 Processing helix chain 'T' and resid 250 through 277 Processing helix chain 'U' and resid 1 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 101 Processing helix chain 'U' and resid 104 through 118 Processing helix chain 'V' and resid 2 through 29 Processing helix chain 'V' and resid 32 through 59 Processing helix chain 'V' and resid 63 through 89 Processing helix chain 'V' and resid 91 through 95 Processing helix chain 'V' and resid 97 through 121 Processing helix chain 'V' and resid 125 through 152 Processing helix chain 'V' and resid 159 through 183 Processing helix chain 'V' and resid 187 through 214 Processing helix chain 'V' and resid 218 through 245 Processing helix chain 'V' and resid 250 through 277 Processing helix chain 'W' and resid 1 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 101 Processing helix chain 'W' and resid 104 through 118 Processing helix chain 'X' and resid 2 through 29 Processing helix chain 'X' and resid 32 through 59 Processing helix chain 'X' and resid 63 through 89 Processing helix chain 'X' and resid 91 through 95 Processing helix chain 'X' and resid 97 through 121 Processing helix chain 'X' and resid 125 through 152 Processing helix chain 'X' and resid 159 through 183 Processing helix chain 'X' and resid 187 through 214 Processing helix chain 'X' and resid 218 through 245 Processing helix chain 'X' and resid 250 through 277 3504 hydrogen bonds defined for protein. 10440 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: 8.10 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8230 1.32 - 1.45: 10436 1.45 - 1.58: 18510 1.58 - 1.70: 12 1.70 - 1.83: 240 Bond restraints: 37428 Sorted by residual: bond pdb=" CB HIS T 92 " pdb=" CG HIS T 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB HIS N 92 " pdb=" CG HIS N 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB HIS P 92 " pdb=" CG HIS P 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS B 92 " pdb=" CG HIS B 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS X 92 " pdb=" CG HIS X 92 " ideal model delta sigma weight residual 1.497 1.441 0.056 1.40e-02 5.10e+03 1.63e+01 ... (remaining 37423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 42226 1.80 - 3.61: 7287 3.61 - 5.41: 827 5.41 - 7.21: 156 7.21 - 9.02: 72 Bond angle restraints: 50568 Sorted by residual: angle pdb=" C ASP M 67 " pdb=" N PRO M 68 " pdb=" CA PRO M 68 " ideal model delta sigma weight residual 119.82 127.54 -7.72 9.80e-01 1.04e+00 6.20e+01 angle pdb=" C ASP C 67 " pdb=" N PRO C 68 " pdb=" CA PRO C 68 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" C ASP A 67 " pdb=" N PRO A 68 " pdb=" CA PRO A 68 " ideal model delta sigma weight residual 119.82 127.52 -7.70 9.80e-01 1.04e+00 6.17e+01 angle pdb=" C ASP I 67 " pdb=" N PRO I 68 " pdb=" CA PRO I 68 " ideal model delta sigma weight residual 119.82 127.51 -7.69 9.80e-01 1.04e+00 6.16e+01 angle pdb=" C ASP W 67 " pdb=" N PRO W 68 " pdb=" CA PRO W 68 " ideal model delta sigma weight residual 119.82 127.51 -7.69 9.80e-01 1.04e+00 6.16e+01 ... (remaining 50563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.37: 21652 12.37 - 24.75: 1388 24.75 - 37.12: 84 37.12 - 49.50: 63 49.50 - 61.87: 81 Dihedral angle restraints: 23268 sinusoidal: 8952 harmonic: 14316 Sorted by residual: dihedral pdb=" C THR N 94 " pdb=" N THR N 94 " pdb=" CA THR N 94 " pdb=" CB THR N 94 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C THR L 94 " pdb=" N THR L 94 " pdb=" CA THR L 94 " pdb=" CB THR L 94 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C THR F 94 " pdb=" N THR F 94 " pdb=" CA THR F 94 " pdb=" CB THR F 94 " ideal model delta harmonic sigma weight residual -122.00 -130.89 8.89 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 23265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4032 0.076 - 0.152: 1521 0.152 - 0.228: 351 0.228 - 0.304: 24 0.304 - 0.380: 36 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CA ASP F 152 " pdb=" N ASP F 152 " pdb=" C ASP F 152 " pdb=" CB ASP F 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ASP V 152 " pdb=" N ASP V 152 " pdb=" C ASP V 152 " pdb=" CB ASP V 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA ASP X 152 " pdb=" N ASP X 152 " pdb=" C ASP X 152 " pdb=" CB ASP X 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5961 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 93 " -0.062 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR Q 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 93 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 93 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR Q 93 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 93 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 93 " -0.062 2.00e-02 2.50e+03 3.21e-02 2.07e+01 pdb=" CG TYR G 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR G 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR G 93 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR G 93 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR G 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR G 93 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 93 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 93 " -0.062 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR U 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR U 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR U 93 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR U 93 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR U 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR U 93 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR U 93 " -0.044 2.00e-02 2.50e+03 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 20521 2.98 - 3.46: 40953 3.46 - 3.94: 61187 3.94 - 4.42: 75458 4.42 - 4.90: 113052 Nonbonded interactions: 311171 Sorted by model distance: nonbonded pdb=" NZ LYS L 235 " pdb=" OE2 GLU V 7 " model vdw 2.497 3.120 nonbonded pdb=" NZ LYS F 235 " pdb=" OE2 GLU P 7 " model vdw 2.497 3.120 nonbonded pdb=" OE2 GLU H 7 " pdb=" NZ LYS V 235 " model vdw 2.497 3.120 nonbonded pdb=" NZ LYS B 235 " pdb=" OE2 GLU J 7 " model vdw 2.497 3.120 nonbonded pdb=" OE2 GLU D 7 " pdb=" NZ LYS X 235 " model vdw 2.497 3.120 ... (remaining 311166 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.940 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 0.083 37428 Z= 1.064 Angle : 1.388 9.015 50568 Z= 0.949 Chirality : 0.084 0.380 5964 Planarity : 0.008 0.032 6432 Dihedral : 9.310 61.873 13932 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 2.05 (0.10), residues: 4704 helix: 1.50 (0.06), residues: 4236 sheet: None (None), residues: 0 loop : 0.57 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 234 TYR 0.062 0.009 TYR Q 93 PHE 0.019 0.007 PHE T 66 TRP 0.022 0.008 TRP K 74 HIS 0.011 0.004 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.01856 (37428) covalent geometry : angle 1.38787 (50568) hydrogen bonds : bond 0.14339 ( 3504) hydrogen bonds : angle 4.95332 (10440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1526 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8429 (m-30) cc_final: 0.8143 (m-30) REVERT: A 94 TYR cc_start: 0.8614 (m-80) cc_final: 0.8280 (m-80) REVERT: B 45 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7814 (ttm-80) REVERT: B 80 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8676 (mmtt) REVERT: B 226 ILE cc_start: 0.8847 (mt) cc_final: 0.8593 (mm) REVERT: C 33 ASP cc_start: 0.8124 (t0) cc_final: 0.7520 (t0) REVERT: C 52 ASP cc_start: 0.8432 (m-30) cc_final: 0.8173 (m-30) REVERT: C 96 LYS cc_start: 0.8604 (mttp) cc_final: 0.8159 (mtpp) REVERT: D 8 MET cc_start: 0.8641 (mtp) cc_final: 0.8391 (mtm) REVERT: D 80 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8544 (mmtt) REVERT: D 129 MET cc_start: 0.8608 (mtm) cc_final: 0.8368 (ttm) REVERT: E 33 ASP cc_start: 0.8219 (t0) cc_final: 0.7722 (t0) REVERT: E 52 ASP cc_start: 0.8305 (m-30) cc_final: 0.8072 (m-30) REVERT: E 96 LYS cc_start: 0.8417 (mttp) cc_final: 0.8151 (mtpt) REVERT: F 67 MET cc_start: 0.8061 (mtm) cc_final: 0.7771 (mtp) REVERT: F 80 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8571 (mmtt) REVERT: G 52 ASP cc_start: 0.8355 (m-30) cc_final: 0.8095 (m-30) REVERT: G 96 LYS cc_start: 0.8536 (mttp) cc_final: 0.8229 (mtpp) REVERT: H 226 ILE cc_start: 0.8781 (mt) cc_final: 0.8438 (mm) REVERT: I 33 ASP cc_start: 0.8058 (t0) cc_final: 0.7516 (t0) REVERT: J 63 SER cc_start: 0.8418 (m) cc_final: 0.8217 (p) REVERT: J 67 MET cc_start: 0.8167 (mtm) cc_final: 0.7725 (mtp) REVERT: J 86 TYR cc_start: 0.8682 (t80) cc_final: 0.8466 (t80) REVERT: J 129 MET cc_start: 0.8469 (mtm) cc_final: 0.8220 (mtp) REVERT: J 226 ILE cc_start: 0.8875 (mt) cc_final: 0.8448 (mm) REVERT: K 35 ASN cc_start: 0.7911 (m-40) cc_final: 0.7630 (t0) REVERT: K 52 ASP cc_start: 0.8417 (m-30) cc_final: 0.8200 (m-30) REVERT: K 94 TYR cc_start: 0.8453 (m-80) cc_final: 0.8149 (m-80) REVERT: L 129 MET cc_start: 0.8601 (mtm) cc_final: 0.8261 (mtp) REVERT: L 226 ILE cc_start: 0.8816 (mt) cc_final: 0.8446 (mm) REVERT: M 33 ASP cc_start: 0.8201 (t0) cc_final: 0.7731 (t0) REVERT: M 67 ASP cc_start: 0.8592 (t0) cc_final: 0.8304 (t0) REVERT: N 45 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7717 (ttm-80) REVERT: N 63 SER cc_start: 0.8392 (m) cc_final: 0.8135 (p) REVERT: N 67 MET cc_start: 0.8018 (mtm) cc_final: 0.7631 (mtp) REVERT: N 80 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8627 (mmtt) REVERT: N 226 ILE cc_start: 0.8818 (mt) cc_final: 0.8511 (mm) REVERT: O 35 ASN cc_start: 0.7968 (m-40) cc_final: 0.7736 (t0) REVERT: O 48 TYR cc_start: 0.8412 (t80) cc_final: 0.8151 (t80) REVERT: O 96 LYS cc_start: 0.8329 (mttp) cc_final: 0.8001 (mtpp) REVERT: P 8 MET cc_start: 0.8709 (mtp) cc_final: 0.8483 (mtm) REVERT: P 67 MET cc_start: 0.8173 (mtm) cc_final: 0.7839 (mtp) REVERT: P 129 MET cc_start: 0.8420 (mtm) cc_final: 0.8143 (mtp) REVERT: P 226 ILE cc_start: 0.8734 (mt) cc_final: 0.8494 (mm) REVERT: Q 33 ASP cc_start: 0.8195 (t0) cc_final: 0.7687 (t0) REVERT: Q 52 ASP cc_start: 0.8355 (m-30) cc_final: 0.8054 (m-30) REVERT: Q 67 ASP cc_start: 0.8549 (t0) cc_final: 0.8294 (t0) REVERT: R 63 SER cc_start: 0.8554 (m) cc_final: 0.8247 (p) REVERT: R 67 MET cc_start: 0.8248 (mtm) cc_final: 0.7771 (mtp) REVERT: S 33 ASP cc_start: 0.8217 (t0) cc_final: 0.7759 (t0) REVERT: S 48 TYR cc_start: 0.8415 (t80) cc_final: 0.8074 (t80) REVERT: S 52 ASP cc_start: 0.8338 (m-30) cc_final: 0.8018 (m-30) REVERT: T 45 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7712 (ttm-80) REVERT: T 67 MET cc_start: 0.8052 (mtm) cc_final: 0.7828 (mtp) REVERT: T 129 MET cc_start: 0.8540 (mtm) cc_final: 0.8320 (mtp) REVERT: T 226 ILE cc_start: 0.8859 (mt) cc_final: 0.8620 (mm) REVERT: U 33 ASP cc_start: 0.8090 (t0) cc_final: 0.7662 (t0) REVERT: U 52 ASP cc_start: 0.8328 (m-30) cc_final: 0.8083 (m-30) REVERT: V 63 SER cc_start: 0.8501 (m) cc_final: 0.8229 (p) REVERT: V 67 MET cc_start: 0.8037 (mtm) cc_final: 0.7700 (mtp) REVERT: V 80 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8526 (mmtt) REVERT: V 129 MET cc_start: 0.8569 (mtm) cc_final: 0.8341 (mtm) REVERT: W 52 ASP cc_start: 0.8340 (m-30) cc_final: 0.8116 (m-30) REVERT: W 67 ASP cc_start: 0.8535 (t0) cc_final: 0.8290 (t0) REVERT: W 94 TYR cc_start: 0.8467 (m-80) cc_final: 0.8225 (m-80) REVERT: X 67 MET cc_start: 0.8071 (mtm) cc_final: 0.7817 (mtp) REVERT: X 80 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8532 (mmtt) REVERT: X 129 MET cc_start: 0.8628 (mtm) cc_final: 0.8291 (mtp) outliers start: 0 outliers final: 0 residues processed: 1526 average time/residue: 0.2815 time to fit residues: 651.9624 Evaluate side-chains 747 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN B 216 HIS D 184 ASN D 216 HIS E 109 GLN E 118 GLN F 184 ASN H 184 ASN H 216 HIS I 118 GLN J 184 ASN J 216 HIS K 118 GLN L 184 ASN L 216 HIS N 184 ASN N 216 HIS O 118 GLN P 184 ASN P 216 HIS R 184 ASN R 216 HIS S 118 GLN T 184 ASN T 216 HIS U 118 GLN V 184 ASN V 216 HIS W 118 GLN X 184 ASN X 216 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120933 restraints weight = 72490.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121584 restraints weight = 64524.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121670 restraints weight = 59206.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121895 restraints weight = 57959.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121916 restraints weight = 56227.190| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37428 Z= 0.155 Angle : 0.565 9.308 50568 Z= 0.312 Chirality : 0.039 0.235 5964 Planarity : 0.004 0.031 6432 Dihedral : 3.479 16.837 5160 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.38 % Allowed : 10.16 % Favored : 88.46 % 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: 4.34 (0.11), residues: 4704 helix: 3.08 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : 0.21 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 234 TYR 0.023 0.002 TYR E 94 PHE 0.024 0.002 PHE H 97 TRP 0.016 0.003 TRP K 40 HIS 0.005 0.001 HIS T 185 Details of bonding type rmsd covalent geometry : bond 0.00330 (37428) covalent geometry : angle 0.56475 (50568) hydrogen bonds : bond 0.04833 ( 3504) hydrogen bonds : angle 3.34206 (10440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1024 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8624 (m-40) cc_final: 0.8302 (m-40) REVERT: B 80 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7896 (mmtp) REVERT: B 150 LEU cc_start: 0.8542 (mt) cc_final: 0.8274 (mt) REVERT: D 8 MET cc_start: 0.8066 (mtp) cc_final: 0.7244 (mtm) REVERT: D 150 LEU cc_start: 0.8559 (mt) cc_final: 0.8272 (mt) REVERT: E 96 LYS cc_start: 0.8661 (mttp) cc_final: 0.8456 (mtpp) REVERT: F 80 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7866 (mmtp) REVERT: F 129 MET cc_start: 0.7579 (mtp) cc_final: 0.7313 (mtp) REVERT: F 150 LEU cc_start: 0.8734 (mt) cc_final: 0.8478 (mt) REVERT: F 226 ILE cc_start: 0.8508 (mm) cc_final: 0.8242 (mm) REVERT: H 67 MET cc_start: 0.7174 (mtp) cc_final: 0.6905 (mtp) REVERT: H 150 LEU cc_start: 0.8725 (mt) cc_final: 0.8345 (mt) REVERT: J 63 SER cc_start: 0.8160 (m) cc_final: 0.7899 (m) REVERT: J 67 MET cc_start: 0.7569 (mtm) cc_final: 0.7012 (mtp) REVERT: J 150 LEU cc_start: 0.8620 (mt) cc_final: 0.8289 (mt) REVERT: K 110 ASN cc_start: 0.8657 (m-40) cc_final: 0.8372 (m-40) REVERT: L 149 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7205 (mtp180) REVERT: L 150 LEU cc_start: 0.8525 (mt) cc_final: 0.8312 (mt) REVERT: N 63 SER cc_start: 0.8218 (m) cc_final: 0.7973 (m) REVERT: N 67 MET cc_start: 0.7541 (mtm) cc_final: 0.7086 (mtp) REVERT: N 150 LEU cc_start: 0.8845 (mt) cc_final: 0.8490 (mt) REVERT: P 67 MET cc_start: 0.7637 (mtm) cc_final: 0.7247 (mtp) REVERT: P 150 LEU cc_start: 0.8742 (mt) cc_final: 0.8426 (mt) REVERT: P 183 SER cc_start: 0.8595 (p) cc_final: 0.8319 (t) REVERT: R 63 SER cc_start: 0.8102 (m) cc_final: 0.7864 (m) REVERT: R 67 MET cc_start: 0.7812 (mtm) cc_final: 0.7368 (mtp) REVERT: S 48 TYR cc_start: 0.8126 (t80) cc_final: 0.7779 (t80) REVERT: T 67 MET cc_start: 0.7403 (mtm) cc_final: 0.7156 (mtp) REVERT: V 63 SER cc_start: 0.8190 (m) cc_final: 0.7862 (m) REVERT: V 67 MET cc_start: 0.7594 (mtm) cc_final: 0.7116 (mtp) REVERT: V 80 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7771 (mmtp) REVERT: V 150 LEU cc_start: 0.8531 (mt) cc_final: 0.8213 (mt) REVERT: W 110 ASN cc_start: 0.8617 (m110) cc_final: 0.8235 (m-40) REVERT: X 67 MET cc_start: 0.7618 (mtm) cc_final: 0.7411 (mtp) REVERT: X 80 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7675 (mmtp) REVERT: X 148 TYR cc_start: 0.8641 (t80) cc_final: 0.8441 (t80) REVERT: X 150 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8162 (mp) REVERT: X 157 ASP cc_start: 0.7126 (p0) cc_final: 0.6870 (p0) REVERT: X 207 GLU cc_start: 0.7277 (tt0) cc_final: 0.7068 (tt0) outliers start: 50 outliers final: 18 residues processed: 1052 average time/residue: 0.2306 time to fit residues: 395.2361 Evaluate side-chains 725 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 706 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 314 optimal weight: 0.8980 chunk 336 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 449 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 367 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN D 60 ASN F 185 HIS H 185 HIS I 118 GLN M 118 GLN P 185 HIS R 185 HIS T 60 ASN W 118 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.141266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121917 restraints weight = 76810.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123235 restraints weight = 61413.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124211 restraints weight = 53210.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124877 restraints weight = 48418.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125133 restraints weight = 45235.822| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37428 Z= 0.132 Angle : 0.494 11.459 50568 Z= 0.272 Chirality : 0.036 0.160 5964 Planarity : 0.003 0.049 6432 Dihedral : 3.365 15.921 5160 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.41 % Allowed : 13.12 % Favored : 85.47 % 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: 4.29 (0.11), residues: 4704 helix: 3.08 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.12 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 32 TYR 0.019 0.001 TYR P 210 PHE 0.013 0.001 PHE T 97 TRP 0.014 0.002 TRP Q 40 HIS 0.005 0.002 HIS P 185 Details of bonding type rmsd covalent geometry : bond 0.00279 (37428) covalent geometry : angle 0.49394 (50568) hydrogen bonds : bond 0.04080 ( 3504) hydrogen bonds : angle 3.26926 (10440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 901 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8785 (m-40) cc_final: 0.8526 (m-40) REVERT: B 80 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8068 (mmtm) REVERT: B 98 MET cc_start: 0.5268 (mmt) cc_final: 0.4543 (mmt) REVERT: B 157 ASP cc_start: 0.6630 (p0) cc_final: 0.6170 (p0) REVERT: C 48 TYR cc_start: 0.8166 (t80) cc_final: 0.7963 (t80) REVERT: D 8 MET cc_start: 0.8210 (mtp) cc_final: 0.7777 (mtm) REVERT: D 152 ASP cc_start: 0.7648 (t0) cc_final: 0.7178 (t70) REVERT: D 157 ASP cc_start: 0.6956 (p0) cc_final: 0.6473 (p0) REVERT: E 32 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8329 (mpt-90) REVERT: E 48 TYR cc_start: 0.8219 (t80) cc_final: 0.7975 (t80) REVERT: E 96 LYS cc_start: 0.8604 (mttp) cc_final: 0.8341 (mtpp) REVERT: F 61 LEU cc_start: 0.8347 (mt) cc_final: 0.8102 (mt) REVERT: F 67 MET cc_start: 0.7574 (mtp) cc_final: 0.7349 (mtp) REVERT: F 80 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8073 (mmtp) REVERT: F 149 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7132 (mtp85) REVERT: F 150 LEU cc_start: 0.8685 (mt) cc_final: 0.8481 (mt) REVERT: F 226 ILE cc_start: 0.8827 (mm) cc_final: 0.8545 (mm) REVERT: H 98 MET cc_start: 0.5832 (mtt) cc_final: 0.5389 (mtp) REVERT: J 60 ASN cc_start: 0.7890 (m-40) cc_final: 0.7552 (t0) REVERT: J 63 SER cc_start: 0.8347 (m) cc_final: 0.8074 (m) REVERT: J 67 MET cc_start: 0.7908 (mtm) cc_final: 0.7445 (mtp) REVERT: J 149 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7215 (mtp180) REVERT: J 157 ASP cc_start: 0.7031 (p0) cc_final: 0.6762 (p0) REVERT: J 226 ILE cc_start: 0.8475 (mm) cc_final: 0.8248 (mm) REVERT: K 98 LEU cc_start: 0.7803 (mt) cc_final: 0.7587 (mt) REVERT: L 149 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7251 (mtp180) REVERT: L 157 ASP cc_start: 0.6911 (p0) cc_final: 0.6316 (p0) REVERT: N 63 SER cc_start: 0.8418 (m) cc_final: 0.8091 (m) REVERT: N 67 MET cc_start: 0.7872 (mtm) cc_final: 0.7391 (mtp) REVERT: N 149 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7368 (mtm180) REVERT: P 67 MET cc_start: 0.7841 (mtm) cc_final: 0.7426 (mtp) REVERT: P 150 LEU cc_start: 0.8588 (mt) cc_final: 0.8342 (mt) REVERT: P 152 ASP cc_start: 0.7737 (t70) cc_final: 0.7386 (t70) REVERT: P 157 ASP cc_start: 0.6913 (p0) cc_final: 0.6460 (p0) REVERT: R 67 MET cc_start: 0.8040 (mtm) cc_final: 0.7604 (mtp) REVERT: R 152 ASP cc_start: 0.7543 (t0) cc_final: 0.7270 (t70) REVERT: R 157 ASP cc_start: 0.6829 (p0) cc_final: 0.6520 (p0) REVERT: R 230 GLU cc_start: 0.6525 (pt0) cc_final: 0.6310 (pt0) REVERT: S 48 TYR cc_start: 0.8254 (t80) cc_final: 0.7994 (t80) REVERT: S 118 GLN cc_start: 0.8088 (tt0) cc_final: 0.7844 (tt0) REVERT: T 67 MET cc_start: 0.7622 (mtm) cc_final: 0.7400 (mtp) REVERT: T 98 MET cc_start: 0.5249 (mmt) cc_final: 0.4962 (mmt) REVERT: T 150 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8196 (mp) REVERT: T 157 ASP cc_start: 0.7038 (p0) cc_final: 0.6738 (p0) REVERT: T 226 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8358 (mm) REVERT: T 230 GLU cc_start: 0.6558 (pt0) cc_final: 0.6305 (pt0) REVERT: V 63 SER cc_start: 0.8263 (m) cc_final: 0.7943 (m) REVERT: V 67 MET cc_start: 0.7792 (mtm) cc_final: 0.7319 (mtp) REVERT: V 152 ASP cc_start: 0.7803 (t70) cc_final: 0.7481 (t70) REVERT: V 157 ASP cc_start: 0.7100 (p0) cc_final: 0.6832 (p0) REVERT: X 67 MET cc_start: 0.7833 (mtm) cc_final: 0.7578 (mtp) REVERT: X 80 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7878 (mmtp) REVERT: X 212 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8164 (mm) REVERT: X 226 ILE cc_start: 0.8362 (mm) cc_final: 0.8152 (mm) outliers start: 51 outliers final: 18 residues processed: 932 average time/residue: 0.2172 time to fit residues: 332.8070 Evaluate side-chains 728 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 707 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain X residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 380 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 325 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN D 123 HIS D 185 HIS H 60 ASN J 107 ASN J 185 HIS L 60 ASN N 60 ASN N 123 HIS P 60 ASN R 60 ASN T 185 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114619 restraints weight = 73646.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115279 restraints weight = 64327.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115913 restraints weight = 59038.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116192 restraints weight = 55590.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116292 restraints weight = 53539.528| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37428 Z= 0.146 Angle : 0.520 11.877 50568 Z= 0.278 Chirality : 0.037 0.192 5964 Planarity : 0.003 0.037 6432 Dihedral : 3.371 16.631 5160 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.83 % Allowed : 15.70 % Favored : 82.48 % 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: 4.21 (0.11), residues: 4704 helix: 3.05 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 32 TYR 0.021 0.001 TYR P 210 PHE 0.010 0.001 PHE F 97 TRP 0.014 0.002 TRP U 40 HIS 0.005 0.001 HIS T 185 Details of bonding type rmsd covalent geometry : bond 0.00332 (37428) covalent geometry : angle 0.51995 (50568) hydrogen bonds : bond 0.03903 ( 3504) hydrogen bonds : angle 3.30679 (10440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 814 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8263 (mt0) cc_final: 0.8034 (mt0) REVERT: A 110 ASN cc_start: 0.8843 (m-40) cc_final: 0.8583 (m-40) REVERT: B 80 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7990 (mmtm) REVERT: B 98 MET cc_start: 0.5343 (mmt) cc_final: 0.4658 (mmt) REVERT: B 149 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7287 (mtp180) REVERT: B 150 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 157 ASP cc_start: 0.6646 (p0) cc_final: 0.6350 (p0) REVERT: D 8 MET cc_start: 0.8250 (mtp) cc_final: 0.7810 (mtm) REVERT: D 150 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7793 (mp) REVERT: D 152 ASP cc_start: 0.7728 (t0) cc_final: 0.7276 (t70) REVERT: D 157 ASP cc_start: 0.7134 (p0) cc_final: 0.6902 (p0) REVERT: E 32 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8435 (mpt-90) REVERT: E 96 LYS cc_start: 0.8629 (mttp) cc_final: 0.8413 (mtpp) REVERT: F 67 MET cc_start: 0.7758 (mtp) cc_final: 0.7496 (mtp) REVERT: F 80 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8066 (mmtp) REVERT: F 157 ASP cc_start: 0.6946 (p0) cc_final: 0.6616 (p0) REVERT: F 160 MET cc_start: 0.6014 (mtp) cc_final: 0.5667 (mtp) REVERT: F 226 ILE cc_start: 0.8777 (mm) cc_final: 0.8538 (mm) REVERT: H 23 LEU cc_start: 0.8998 (mm) cc_final: 0.8764 (mm) REVERT: H 98 MET cc_start: 0.5769 (mtt) cc_final: 0.5283 (mtp) REVERT: H 157 ASP cc_start: 0.6841 (p0) cc_final: 0.6381 (p0) REVERT: J 60 ASN cc_start: 0.7946 (m-40) cc_final: 0.7707 (t0) REVERT: J 63 SER cc_start: 0.8571 (m) cc_final: 0.8314 (m) REVERT: J 67 MET cc_start: 0.7892 (mtm) cc_final: 0.7357 (mtp) REVERT: J 149 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7114 (mtm180) REVERT: L 23 LEU cc_start: 0.8949 (mm) cc_final: 0.8720 (mm) REVERT: L 149 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7278 (mtp180) REVERT: N 63 SER cc_start: 0.8594 (m) cc_final: 0.8300 (m) REVERT: N 67 MET cc_start: 0.7899 (mtm) cc_final: 0.7485 (mtp) REVERT: N 98 MET cc_start: 0.5556 (mtt) cc_final: 0.5320 (mtp) REVERT: N 246 ASN cc_start: 0.6958 (t0) cc_final: 0.6611 (t0) REVERT: P 23 LEU cc_start: 0.8917 (mm) cc_final: 0.8652 (mm) REVERT: P 67 MET cc_start: 0.7791 (mtm) cc_final: 0.7506 (mtp) REVERT: P 150 LEU cc_start: 0.8680 (mt) cc_final: 0.8428 (mt) REVERT: P 191 MET cc_start: 0.7903 (mtt) cc_final: 0.7615 (mtt) REVERT: P 260 ILE cc_start: 0.8365 (mt) cc_final: 0.8159 (mt) REVERT: Q 32 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8475 (tpp80) REVERT: R 23 LEU cc_start: 0.8892 (mm) cc_final: 0.8661 (mm) REVERT: R 67 MET cc_start: 0.8075 (mtm) cc_final: 0.7681 (mtp) REVERT: R 152 ASP cc_start: 0.7692 (t0) cc_final: 0.7389 (t70) REVERT: T 2 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7269 (mp0) REVERT: T 67 MET cc_start: 0.7832 (mtm) cc_final: 0.7544 (mtp) REVERT: T 98 MET cc_start: 0.5470 (mmt) cc_final: 0.5167 (mmt) REVERT: T 150 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8268 (mp) REVERT: V 23 LEU cc_start: 0.8837 (mm) cc_final: 0.8627 (mm) REVERT: V 63 SER cc_start: 0.8374 (m) cc_final: 0.8101 (m) REVERT: V 67 MET cc_start: 0.7927 (mtm) cc_final: 0.7447 (mtp) REVERT: V 98 MET cc_start: 0.5450 (mtt) cc_final: 0.5158 (mtp) REVERT: V 100 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7674 (mpt180) REVERT: V 152 ASP cc_start: 0.8021 (t70) cc_final: 0.7761 (t70) REVERT: V 266 LEU cc_start: 0.8532 (mt) cc_final: 0.8199 (mt) REVERT: X 67 MET cc_start: 0.7927 (mtm) cc_final: 0.7671 (mtp) REVERT: X 80 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7928 (mmtp) REVERT: X 157 ASP cc_start: 0.7033 (p0) cc_final: 0.6666 (p0) REVERT: X 243 LEU cc_start: 0.8842 (mp) cc_final: 0.8638 (mp) outliers start: 66 outliers final: 31 residues processed: 853 average time/residue: 0.2189 time to fit residues: 305.7337 Evaluate side-chains 720 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 686 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 258 optimal weight: 4.9990 chunk 370 optimal weight: 0.8980 chunk 434 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 chunk 350 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 428 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 439 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 109 GLN F 123 HIS H 123 HIS H 246 ASN J 123 HIS L 123 HIS L 185 HIS P 123 HIS R 123 HIS V 123 HIS V 185 HIS X 123 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118595 restraints weight = 73347.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118772 restraints weight = 70145.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118730 restraints weight = 67127.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118765 restraints weight = 66252.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118805 restraints weight = 65507.372| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 37428 Z= 0.117 Angle : 0.497 13.226 50568 Z= 0.267 Chirality : 0.036 0.270 5964 Planarity : 0.003 0.031 6432 Dihedral : 3.267 14.910 5160 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.69 % Allowed : 16.92 % Favored : 81.40 % 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: 4.23 (0.11), residues: 4704 helix: 3.07 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.56 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 100 TYR 0.017 0.001 TYR P 210 PHE 0.008 0.001 PHE X 97 TRP 0.012 0.002 TRP G 40 HIS 0.003 0.001 HIS H 123 Details of bonding type rmsd covalent geometry : bond 0.00247 (37428) covalent geometry : angle 0.49744 (50568) hydrogen bonds : bond 0.03529 ( 3504) hydrogen bonds : angle 3.26337 (10440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 853 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8226 (mt0) cc_final: 0.8000 (mt0) REVERT: A 110 ASN cc_start: 0.8802 (m-40) cc_final: 0.8586 (m-40) REVERT: B 80 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7888 (mmtm) REVERT: B 98 MET cc_start: 0.5084 (mmt) cc_final: 0.4565 (mmt) REVERT: B 150 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 157 ASP cc_start: 0.6604 (p0) cc_final: 0.6366 (p0) REVERT: C 32 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.7533 (mpt-90) REVERT: D 8 MET cc_start: 0.8167 (mtp) cc_final: 0.7621 (mtm) REVERT: D 114 LEU cc_start: 0.8305 (mt) cc_final: 0.8090 (mt) REVERT: D 150 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7864 (mp) REVERT: D 152 ASP cc_start: 0.7611 (t0) cc_final: 0.7223 (t70) REVERT: E 32 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8292 (mpt-90) REVERT: E 96 LYS cc_start: 0.8664 (mttp) cc_final: 0.8443 (mtpp) REVERT: E 115 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7805 (ttm) REVERT: F 80 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7936 (mmtp) REVERT: H 23 LEU cc_start: 0.8925 (mm) cc_final: 0.8564 (mm) REVERT: H 98 MET cc_start: 0.5475 (mtt) cc_final: 0.5099 (mtp) REVERT: J 63 SER cc_start: 0.8352 (m) cc_final: 0.8046 (m) REVERT: J 67 MET cc_start: 0.7843 (mtm) cc_final: 0.7342 (mtp) REVERT: J 149 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.7126 (mtp180) REVERT: K 32 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8024 (mpt-90) REVERT: L 23 LEU cc_start: 0.8875 (mm) cc_final: 0.8583 (mm) REVERT: L 86 TYR cc_start: 0.8059 (t80) cc_final: 0.6868 (t80) REVERT: L 149 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7206 (mtp180) REVERT: N 67 MET cc_start: 0.7825 (mtm) cc_final: 0.7421 (mtp) REVERT: N 98 MET cc_start: 0.5357 (mtt) cc_final: 0.5140 (mtp) REVERT: N 157 ASP cc_start: 0.6931 (p0) cc_final: 0.6711 (p0) REVERT: O 61 GLN cc_start: 0.8286 (mt0) cc_final: 0.8084 (mt0) REVERT: P 23 LEU cc_start: 0.8891 (mm) cc_final: 0.8675 (mm) REVERT: P 150 LEU cc_start: 0.8672 (mt) cc_final: 0.8441 (mt) REVERT: R 23 LEU cc_start: 0.8794 (mm) cc_final: 0.8367 (mm) REVERT: R 67 MET cc_start: 0.7995 (mtm) cc_final: 0.7622 (mtp) REVERT: R 152 ASP cc_start: 0.7839 (t0) cc_final: 0.7557 (t70) REVERT: R 157 ASP cc_start: 0.6851 (p0) cc_final: 0.6347 (p0) REVERT: S 14 TYR cc_start: 0.8755 (t80) cc_final: 0.8269 (t80) REVERT: T 67 MET cc_start: 0.7706 (mtm) cc_final: 0.7385 (mtp) REVERT: T 150 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8323 (mp) REVERT: U 32 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.7565 (mpt-90) REVERT: V 23 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8322 (mm) REVERT: V 63 SER cc_start: 0.8263 (m) cc_final: 0.7932 (m) REVERT: V 67 MET cc_start: 0.7847 (mtm) cc_final: 0.7344 (mtp) REVERT: V 98 MET cc_start: 0.5429 (mtt) cc_final: 0.4993 (mtp) REVERT: V 266 LEU cc_start: 0.8445 (mt) cc_final: 0.8149 (mt) REVERT: W 48 TYR cc_start: 0.8193 (t80) cc_final: 0.7918 (t80) REVERT: X 67 MET cc_start: 0.7855 (mtm) cc_final: 0.7604 (mtp) REVERT: X 80 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7936 (mmtp) REVERT: X 129 MET cc_start: 0.7878 (mtp) cc_final: 0.7677 (mtp) REVERT: X 152 ASP cc_start: 0.7778 (t70) cc_final: 0.7568 (t70) outliers start: 61 outliers final: 33 residues processed: 891 average time/residue: 0.2190 time to fit residues: 317.4582 Evaluate side-chains 753 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 715 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 23 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 235 optimal weight: 10.0000 chunk 370 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 367 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 60 ASN H 60 ASN H 246 ASN J 60 ASN J 184 ASN M 110 ASN P 60 ASN ** P 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118987 restraints weight = 73010.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118901 restraints weight = 70935.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118858 restraints weight = 71056.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118881 restraints weight = 68915.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118928 restraints weight = 68343.941| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37428 Z= 0.123 Angle : 0.522 13.816 50568 Z= 0.280 Chirality : 0.037 0.279 5964 Planarity : 0.003 0.032 6432 Dihedral : 3.261 14.525 5160 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.02 % Allowed : 18.49 % Favored : 79.49 % 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: 4.14 (0.11), residues: 4704 helix: 2.99 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : -0.50 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 211 TYR 0.017 0.001 TYR P 210 PHE 0.007 0.001 PHE X 190 TRP 0.013 0.002 TRP E 40 HIS 0.003 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00269 (37428) covalent geometry : angle 0.52156 (50568) hydrogen bonds : bond 0.03499 ( 3504) hydrogen bonds : angle 3.32589 (10440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 790 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8249 (mt0) cc_final: 0.8014 (mt0) REVERT: A 110 ASN cc_start: 0.8777 (m-40) cc_final: 0.8518 (m-40) REVERT: B 80 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7835 (mmtm) REVERT: B 98 MET cc_start: 0.5018 (mmt) cc_final: 0.4577 (mmt) REVERT: B 149 ARG cc_start: 0.7394 (mtp180) cc_final: 0.7127 (mtp180) REVERT: B 150 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 32 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: D 8 MET cc_start: 0.8101 (mtp) cc_final: 0.7699 (mtm) REVERT: D 150 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7903 (mp) REVERT: F 80 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7870 (mmtp) REVERT: F 98 MET cc_start: 0.5404 (mmt) cc_final: 0.5078 (mmt) REVERT: F 150 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8235 (mp) REVERT: G 96 LYS cc_start: 0.8718 (mttp) cc_final: 0.8462 (mtpp) REVERT: G 115 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7747 (mtm) REVERT: H 23 LEU cc_start: 0.8892 (mm) cc_final: 0.8588 (mm) REVERT: H 34 LYS cc_start: 0.7745 (mmpt) cc_final: 0.7492 (mptt) REVERT: H 98 MET cc_start: 0.5401 (mtt) cc_final: 0.5045 (mtp) REVERT: I 32 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7885 (mpt-90) REVERT: J 63 SER cc_start: 0.8256 (m) cc_final: 0.7982 (m) REVERT: J 67 MET cc_start: 0.7814 (mtm) cc_final: 0.7297 (mtp) REVERT: J 86 TYR cc_start: 0.8088 (t80) cc_final: 0.7474 (t80) REVERT: J 149 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7120 (mtp180) REVERT: L 23 LEU cc_start: 0.8886 (mm) cc_final: 0.8229 (mm) REVERT: M 14 TYR cc_start: 0.8657 (t80) cc_final: 0.8213 (t80) REVERT: N 67 MET cc_start: 0.7817 (mtm) cc_final: 0.7450 (mtp) REVERT: N 86 TYR cc_start: 0.8065 (t80) cc_final: 0.7680 (t80) REVERT: N 98 MET cc_start: 0.5409 (mtt) cc_final: 0.5195 (mtp) REVERT: N 191 MET cc_start: 0.7605 (mpp) cc_final: 0.7336 (mtm) REVERT: O 48 TYR cc_start: 0.8189 (t80) cc_final: 0.7843 (t80) REVERT: P 23 LEU cc_start: 0.8875 (mm) cc_final: 0.8638 (mm) REVERT: P 98 MET cc_start: 0.5330 (mmt) cc_final: 0.5051 (mmt) REVERT: P 150 LEU cc_start: 0.8605 (mt) cc_final: 0.8377 (mt) REVERT: P 207 GLU cc_start: 0.7515 (tt0) cc_final: 0.7252 (tt0) REVERT: R 23 LEU cc_start: 0.8897 (mm) cc_final: 0.8590 (mm) REVERT: R 34 LYS cc_start: 0.7659 (mmpt) cc_final: 0.7394 (mptt) REVERT: R 67 MET cc_start: 0.7982 (mtm) cc_final: 0.7646 (mtp) REVERT: S 14 TYR cc_start: 0.8724 (t80) cc_final: 0.8218 (t80) REVERT: T 67 MET cc_start: 0.7745 (mtm) cc_final: 0.7398 (mtp) REVERT: T 150 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8364 (mp) REVERT: V 23 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8117 (mm) REVERT: V 63 SER cc_start: 0.8329 (m) cc_final: 0.8032 (m) REVERT: V 67 MET cc_start: 0.7842 (mtm) cc_final: 0.7420 (mtp) REVERT: V 98 MET cc_start: 0.5328 (mtt) cc_final: 0.4932 (mtp) REVERT: V 243 LEU cc_start: 0.8627 (mp) cc_final: 0.8418 (mp) REVERT: V 266 LEU cc_start: 0.8512 (mt) cc_final: 0.8125 (mt) REVERT: W 48 TYR cc_start: 0.8171 (t80) cc_final: 0.7968 (t80) REVERT: X 67 MET cc_start: 0.7845 (mtm) cc_final: 0.7616 (mtp) REVERT: X 80 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7890 (mmtp) REVERT: X 129 MET cc_start: 0.7914 (mtp) cc_final: 0.7664 (mtp) REVERT: X 157 ASP cc_start: 0.6592 (p0) cc_final: 0.6261 (p0) outliers start: 73 outliers final: 36 residues processed: 829 average time/residue: 0.2206 time to fit residues: 298.1258 Evaluate side-chains 746 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 704 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 248 THR Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 4 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 389 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS D 60 ASN F 60 ASN H 246 ASN J 184 ASN N 60 ASN ** P 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 184 ASN T 123 HIS T 246 ASN X 246 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117890 restraints weight = 73237.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118387 restraints weight = 65640.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118588 restraints weight = 61277.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119023 restraints weight = 59236.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119057 restraints weight = 57367.090| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37428 Z= 0.126 Angle : 0.539 13.750 50568 Z= 0.287 Chirality : 0.038 0.308 5964 Planarity : 0.003 0.034 6432 Dihedral : 3.264 14.182 5160 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.10 % Allowed : 18.91 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.08 (0.11), residues: 4704 helix: 2.97 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : -0.66 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.013 0.001 TYR L 210 PHE 0.007 0.001 PHE X 190 TRP 0.012 0.002 TRP E 74 HIS 0.003 0.000 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00277 (37428) covalent geometry : angle 0.53901 (50568) hydrogen bonds : bond 0.03446 ( 3504) hydrogen bonds : angle 3.36094 (10440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 766 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8258 (mt0) cc_final: 0.8023 (mt0) REVERT: B 80 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7893 (mmtm) REVERT: B 86 TYR cc_start: 0.8388 (t80) cc_final: 0.8075 (t80) REVERT: B 98 MET cc_start: 0.5049 (mmt) cc_final: 0.4593 (mmt) REVERT: B 149 ARG cc_start: 0.7459 (mtp180) cc_final: 0.7185 (mtp180) REVERT: C 32 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8402 (mmm-85) REVERT: D 8 MET cc_start: 0.8149 (mtp) cc_final: 0.7728 (mtm) REVERT: D 98 MET cc_start: 0.5765 (mtp) cc_final: 0.5472 (mtp) REVERT: D 150 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7861 (mp) REVERT: D 191 MET cc_start: 0.8152 (mpp) cc_final: 0.7939 (mtm) REVERT: F 80 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7908 (mmtp) REVERT: F 98 MET cc_start: 0.5424 (mmt) cc_final: 0.5200 (mmt) REVERT: F 150 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8219 (mp) REVERT: G 96 LYS cc_start: 0.8701 (mttp) cc_final: 0.8410 (mtpp) REVERT: H 23 LEU cc_start: 0.8965 (mm) cc_final: 0.8611 (mm) REVERT: H 34 LYS cc_start: 0.7729 (mmpt) cc_final: 0.7517 (mptt) REVERT: H 98 MET cc_start: 0.5368 (mtt) cc_final: 0.5072 (mtp) REVERT: I 32 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.7910 (mmm-85) REVERT: J 63 SER cc_start: 0.8427 (m) cc_final: 0.8216 (m) REVERT: J 67 MET cc_start: 0.7880 (mtm) cc_final: 0.7363 (mtp) REVERT: J 86 TYR cc_start: 0.8254 (t80) cc_final: 0.6707 (t80) REVERT: J 149 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7157 (mtm180) REVERT: K 32 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8115 (mpt-90) REVERT: L 23 LEU cc_start: 0.8683 (mm) cc_final: 0.8339 (mm) REVERT: M 14 TYR cc_start: 0.8716 (t80) cc_final: 0.8264 (t80) REVERT: N 67 MET cc_start: 0.7930 (mtm) cc_final: 0.7525 (mtp) REVERT: N 98 MET cc_start: 0.5310 (mtt) cc_final: 0.5080 (mtp) REVERT: O 48 TYR cc_start: 0.8220 (t80) cc_final: 0.7886 (t80) REVERT: P 23 LEU cc_start: 0.8947 (mm) cc_final: 0.8293 (mm) REVERT: P 150 LEU cc_start: 0.8695 (mt) cc_final: 0.8410 (mt) REVERT: Q 35 ASN cc_start: 0.7757 (p0) cc_final: 0.7548 (t0) REVERT: R 23 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8588 (mm) REVERT: R 34 LYS cc_start: 0.7733 (mmpt) cc_final: 0.7445 (mptt) REVERT: R 67 MET cc_start: 0.8087 (mtm) cc_final: 0.7707 (mtp) REVERT: R 98 MET cc_start: 0.5068 (mmt) cc_final: 0.4375 (mmt) REVERT: S 14 TYR cc_start: 0.8775 (t80) cc_final: 0.8267 (t80) REVERT: T 67 MET cc_start: 0.7872 (mtm) cc_final: 0.7518 (mtp) REVERT: T 98 MET cc_start: 0.6222 (mtp) cc_final: 0.6022 (mtt) REVERT: T 150 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8258 (mp) REVERT: U 32 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7765 (mpt-90) REVERT: V 67 MET cc_start: 0.7875 (mtm) cc_final: 0.7658 (mtp) REVERT: V 98 MET cc_start: 0.5330 (mtt) cc_final: 0.4907 (mtp) REVERT: V 266 LEU cc_start: 0.8587 (mt) cc_final: 0.8288 (mt) REVERT: X 67 MET cc_start: 0.7935 (mtm) cc_final: 0.7670 (mtp) REVERT: X 80 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7907 (mmtp) REVERT: X 129 MET cc_start: 0.7993 (mtp) cc_final: 0.7753 (mtp) outliers start: 76 outliers final: 45 residues processed: 810 average time/residue: 0.2247 time to fit residues: 298.2260 Evaluate side-chains 733 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 684 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 84 GLN Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 246 ASN Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 128 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 415 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 384 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN D 60 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN H 184 ASN I 61 GLN L 60 ASN L 246 ASN ** P 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 184 ASN X 246 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111129 restraints weight = 73981.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111133 restraints weight = 68973.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111133 restraints weight = 68903.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111133 restraints weight = 68903.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111133 restraints weight = 68901.752| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 37428 Z= 0.248 Angle : 0.706 13.063 50568 Z= 0.364 Chirality : 0.045 0.397 5964 Planarity : 0.004 0.041 6432 Dihedral : 3.635 14.666 5160 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.66 % Allowed : 19.41 % Favored : 77.93 % 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: 3.49 (0.11), residues: 4704 helix: 2.60 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : -1.07 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 211 TYR 0.016 0.002 TYR P 210 PHE 0.013 0.002 PHE X 190 TRP 0.013 0.002 TRP I 40 HIS 0.004 0.001 HIS X 185 Details of bonding type rmsd covalent geometry : bond 0.00607 (37428) covalent geometry : angle 0.70638 (50568) hydrogen bonds : bond 0.04437 ( 3504) hydrogen bonds : angle 3.74921 (10440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 717 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8379 (mt0) cc_final: 0.8163 (mt0) REVERT: B 98 MET cc_start: 0.5197 (mmt) cc_final: 0.4786 (mmt) REVERT: B 150 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 32 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8370 (mmm-85) REVERT: D 8 MET cc_start: 0.8157 (mtp) cc_final: 0.7916 (mtm) REVERT: D 150 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7980 (mp) REVERT: D 191 MET cc_start: 0.8409 (mpp) cc_final: 0.8032 (mtm) REVERT: F 80 LYS cc_start: 0.8424 (mmtt) cc_final: 0.7840 (mmtp) REVERT: F 150 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8351 (mp) REVERT: F 152 ASP cc_start: 0.8193 (t70) cc_final: 0.7908 (t70) REVERT: F 196 MET cc_start: 0.6882 (tpp) cc_final: 0.6637 (tpp) REVERT: G 96 LYS cc_start: 0.8660 (mttp) cc_final: 0.8362 (mtpp) REVERT: H 23 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8617 (mm) REVERT: H 98 MET cc_start: 0.5726 (mtt) cc_final: 0.5348 (mtp) REVERT: J 67 MET cc_start: 0.7935 (mtm) cc_final: 0.7680 (mtm) REVERT: K 21 ILE cc_start: 0.9092 (mm) cc_final: 0.8888 (mm) REVERT: L 23 LEU cc_start: 0.8757 (mm) cc_final: 0.8375 (mm) REVERT: N 67 MET cc_start: 0.7954 (mtm) cc_final: 0.7656 (mtp) REVERT: N 98 MET cc_start: 0.5712 (mtt) cc_final: 0.5462 (mtp) REVERT: P 23 LEU cc_start: 0.8886 (mm) cc_final: 0.8505 (mm) REVERT: P 152 ASP cc_start: 0.7969 (t70) cc_final: 0.7672 (t70) REVERT: R 23 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8660 (mm) REVERT: R 34 LYS cc_start: 0.7799 (mmpt) cc_final: 0.7531 (mptt) REVERT: R 67 MET cc_start: 0.8058 (mtm) cc_final: 0.7654 (mtp) REVERT: R 98 MET cc_start: 0.5258 (mmt) cc_final: 0.5057 (mmt) REVERT: R 152 ASP cc_start: 0.8037 (t0) cc_final: 0.7743 (t70) REVERT: T 98 MET cc_start: 0.6498 (mtp) cc_final: 0.6200 (mtt) REVERT: V 67 MET cc_start: 0.7952 (mtm) cc_final: 0.7629 (mtp) REVERT: V 98 MET cc_start: 0.5714 (mtt) cc_final: 0.5327 (mtp) REVERT: X 67 MET cc_start: 0.7964 (mtm) cc_final: 0.7745 (mtp) REVERT: X 80 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7924 (mmtp) REVERT: X 152 ASP cc_start: 0.7864 (t70) cc_final: 0.7542 (t70) outliers start: 96 outliers final: 56 residues processed: 772 average time/residue: 0.2331 time to fit residues: 290.9163 Evaluate side-chains 720 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 659 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 248 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 248 THR Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 7 GLU Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 246 ASN Chi-restraints excluded: chain X residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 213 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 260 optimal weight: 0.0070 chunk 379 optimal weight: 0.9990 chunk 364 optimal weight: 0.4980 chunk 255 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN D 60 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN I 61 GLN J 184 ASN L 246 ASN ** P 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN T 246 ASN X 246 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116079 restraints weight = 73774.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116590 restraints weight = 67344.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116870 restraints weight = 63013.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116869 restraints weight = 60592.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116869 restraints weight = 60589.647| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37428 Z= 0.136 Angle : 0.610 15.206 50568 Z= 0.324 Chirality : 0.041 0.335 5964 Planarity : 0.003 0.038 6432 Dihedral : 3.476 19.847 5160 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.63 % Allowed : 21.32 % Favored : 77.05 % 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: 3.65 (0.12), residues: 4704 helix: 2.71 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -1.03 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 100 TYR 0.036 0.001 TYR V 210 PHE 0.010 0.001 PHE X 190 TRP 0.012 0.002 TRP I 40 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00301 (37428) covalent geometry : angle 0.61035 (50568) hydrogen bonds : bond 0.03709 ( 3504) hydrogen bonds : angle 3.60246 (10440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 739 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8248 (mt0) cc_final: 0.7991 (mt0) REVERT: B 98 MET cc_start: 0.4976 (mmt) cc_final: 0.4695 (mmt) REVERT: C 32 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8316 (mmm-85) REVERT: D 8 MET cc_start: 0.8166 (mtp) cc_final: 0.7761 (mtm) REVERT: D 98 MET cc_start: 0.5780 (mtp) cc_final: 0.5490 (mtp) REVERT: D 150 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 157 ASP cc_start: 0.6603 (p0) cc_final: 0.6384 (p0) REVERT: E 62 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8816 (mmmm) REVERT: E 72 GLU cc_start: 0.7530 (mp0) cc_final: 0.7204 (mp0) REVERT: F 80 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7904 (mmtp) REVERT: F 150 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8257 (mp) REVERT: F 152 ASP cc_start: 0.8170 (t70) cc_final: 0.7886 (t70) REVERT: G 96 LYS cc_start: 0.8690 (mttp) cc_final: 0.8450 (mtpp) REVERT: H 23 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8353 (mm) REVERT: H 98 MET cc_start: 0.5686 (mtt) cc_final: 0.5371 (mtp) REVERT: J 8 MET cc_start: 0.8369 (mtp) cc_final: 0.7964 (mtm) REVERT: J 107 ASN cc_start: 0.7424 (p0) cc_final: 0.7222 (p0) REVERT: J 149 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7027 (mtp180) REVERT: K 54 ASP cc_start: 0.8281 (m-30) cc_final: 0.7970 (m-30) REVERT: L 23 LEU cc_start: 0.8725 (mm) cc_final: 0.8360 (mm) REVERT: N 67 MET cc_start: 0.7987 (mtm) cc_final: 0.7632 (mtp) REVERT: O 48 TYR cc_start: 0.8271 (t80) cc_final: 0.7905 (t80) REVERT: P 23 LEU cc_start: 0.8760 (mm) cc_final: 0.8381 (mm) REVERT: P 152 ASP cc_start: 0.8068 (t70) cc_final: 0.7767 (t70) REVERT: R 23 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8146 (mm) REVERT: R 34 LYS cc_start: 0.7793 (mmpt) cc_final: 0.7573 (mptt) REVERT: R 67 MET cc_start: 0.8187 (mtm) cc_final: 0.7800 (mtp) REVERT: U 32 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7634 (mpt-90) REVERT: V 67 MET cc_start: 0.7952 (mtm) cc_final: 0.7590 (mtp) REVERT: V 98 MET cc_start: 0.5467 (mtt) cc_final: 0.4979 (mtp) REVERT: V 266 LEU cc_start: 0.8734 (mt) cc_final: 0.8416 (mt) REVERT: X 67 MET cc_start: 0.8015 (mtm) cc_final: 0.7806 (mtp) REVERT: X 80 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7905 (mmtp) REVERT: X 152 ASP cc_start: 0.7805 (t70) cc_final: 0.7572 (t70) outliers start: 59 outliers final: 40 residues processed: 775 average time/residue: 0.2265 time to fit residues: 286.2068 Evaluate side-chains 718 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 674 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 248 THR Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 246 ASN Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 246 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 393 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 431 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 246 ASN F 216 HIS J 60 ASN J 184 ASN L 246 ASN ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN X 246 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111015 restraints weight = 74465.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111317 restraints weight = 68752.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111357 restraints weight = 65822.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111357 restraints weight = 65149.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111357 restraints weight = 65150.008| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 37428 Z= 0.232 Angle : 0.736 14.070 50568 Z= 0.382 Chirality : 0.047 0.481 5964 Planarity : 0.004 0.043 6432 Dihedral : 3.754 20.562 5160 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.63 % Allowed : 21.57 % Favored : 76.80 % 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: 3.19 (0.12), residues: 4704 helix: 2.43 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -1.48 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 149 TYR 0.029 0.002 TYR T 210 PHE 0.012 0.002 PHE J 128 TRP 0.011 0.002 TRP I 40 HIS 0.004 0.001 HIS N 185 Details of bonding type rmsd covalent geometry : bond 0.00569 (37428) covalent geometry : angle 0.73624 (50568) hydrogen bonds : bond 0.04472 ( 3504) hydrogen bonds : angle 3.90114 (10440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 691 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8430 (mt0) cc_final: 0.8208 (mt0) REVERT: B 98 MET cc_start: 0.5148 (mmt) cc_final: 0.4748 (mmt) REVERT: C 32 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8315 (mmm-85) REVERT: D 8 MET cc_start: 0.8169 (mtp) cc_final: 0.7910 (mtm) REVERT: D 98 MET cc_start: 0.5866 (mtp) cc_final: 0.5611 (mtp) REVERT: D 150 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8037 (mp) REVERT: F 80 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7895 (mmtp) REVERT: F 150 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8269 (mp) REVERT: F 152 ASP cc_start: 0.8290 (t70) cc_final: 0.8004 (t70) REVERT: G 96 LYS cc_start: 0.8612 (mttp) cc_final: 0.8388 (mtpp) REVERT: H 23 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8404 (mm) REVERT: H 98 MET cc_start: 0.5734 (mtt) cc_final: 0.5434 (mtp) REVERT: J 8 MET cc_start: 0.8418 (mtp) cc_final: 0.8146 (mtm) REVERT: J 149 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7051 (mtm180) REVERT: L 23 LEU cc_start: 0.8709 (mm) cc_final: 0.8305 (mm) REVERT: N 67 MET cc_start: 0.7957 (mtm) cc_final: 0.7630 (mtp) REVERT: N 152 ASP cc_start: 0.8112 (t0) cc_final: 0.7804 (t70) REVERT: P 23 LEU cc_start: 0.8872 (mm) cc_final: 0.8430 (mm) REVERT: P 98 MET cc_start: 0.6302 (mtt) cc_final: 0.5412 (ttm) REVERT: P 152 ASP cc_start: 0.8222 (t70) cc_final: 0.7884 (t70) REVERT: R 23 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8491 (mm) REVERT: R 34 LYS cc_start: 0.7898 (mmpt) cc_final: 0.7686 (mptt) REVERT: R 67 MET cc_start: 0.8062 (mtm) cc_final: 0.7691 (mtp) REVERT: T 152 ASP cc_start: 0.8204 (t70) cc_final: 0.7962 (t70) REVERT: V 67 MET cc_start: 0.7969 (mtm) cc_final: 0.7654 (mtp) REVERT: V 98 MET cc_start: 0.5610 (mtt) cc_final: 0.5264 (mtp) REVERT: V 152 ASP cc_start: 0.8239 (t70) cc_final: 0.7923 (t0) REVERT: X 67 MET cc_start: 0.7913 (mtm) cc_final: 0.7697 (mtp) REVERT: X 80 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7923 (mmtp) REVERT: X 152 ASP cc_start: 0.7870 (t70) cc_final: 0.7611 (t70) outliers start: 59 outliers final: 44 residues processed: 725 average time/residue: 0.2317 time to fit residues: 271.3247 Evaluate side-chains 692 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 644 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 34 LYS Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 248 THR Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 246 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 289 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 355 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 424 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN N 246 ASN ** P 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN W 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114282 restraints weight = 74020.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114651 restraints weight = 68255.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114995 restraints weight = 64686.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114995 restraints weight = 62035.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114995 restraints weight = 62035.299| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 37428 Z= 0.154 Angle : 0.658 15.495 50568 Z= 0.350 Chirality : 0.044 0.493 5964 Planarity : 0.003 0.042 6432 Dihedral : 3.624 17.426 5160 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.63 % Allowed : 22.34 % Favored : 76.02 % 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: 3.35 (0.12), residues: 4704 helix: 2.54 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -1.43 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 211 TYR 0.029 0.001 TYR T 210 PHE 0.010 0.001 PHE X 190 TRP 0.014 0.002 TRP W 74 HIS 0.003 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00361 (37428) covalent geometry : angle 0.65778 (50568) hydrogen bonds : bond 0.03958 ( 3504) hydrogen bonds : angle 3.76413 (10440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6712.95 seconds wall clock time: 116 minutes 42.01 seconds (7002.01 seconds total)